Merge pull request #4169 from ohenrich/cg-dna
CG-DNA: Real units and potential reader
This commit is contained in:
Axel Kohlmeyer
@ -405,6 +405,7 @@ and :ref:`ASPHERE <PKG-ASPHERE>` packages are installed.
|
||||
* :doc:`bond_style oxdna2/\* <bond_oxdna>`
|
||||
* :doc:`bond_style oxrna2/\* <bond_oxdna>`
|
||||
* :doc:`fix nve/dotc/langevin <fix_nve_dotc_langevin>`
|
||||
* examples/PACKAGES/cgdna
|
||||
|
||||
----------
|
||||
|
||||
|
||||
@ -27,6 +27,7 @@ Examples
|
||||
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
# LJ units
|
||||
bond_style oxdna/fene
|
||||
bond_coeff * 2.0 0.25 0.7525
|
||||
|
||||
@ -36,6 +37,32 @@ Examples
|
||||
bond_style oxrna2/fene
|
||||
bond_coeff * 2.0 0.25 0.76107
|
||||
|
||||
bond_style oxdna/fene
|
||||
bond_coeff * oxdna_lj.cgdna
|
||||
|
||||
# Real units
|
||||
bond_style oxdna/fene
|
||||
bond_coeff * 11.92337812042065 2.1295 6.409795
|
||||
|
||||
bond_style oxdna2/fene
|
||||
bond_coeff * 11.92337812042065 2.1295 6.4430152
|
||||
|
||||
bond_style oxrna2/fene
|
||||
bond_coeff * 11.92337812042065 2.1295 6.482800913
|
||||
|
||||
bond_style oxrna2/fene
|
||||
bond_coeff * oxrna2_real.cgdna
|
||||
|
||||
.. note::
|
||||
|
||||
The coefficients in the above examples have to be kept fixed and
|
||||
cannot be changed without reparameterizing the entire model. They are
|
||||
provided in forms compatible with both *units lj* and *units real*
|
||||
(see documentation of :doc:`units <units>`). These can also be read
|
||||
from a potential file with correct unit style by specifying the name
|
||||
of the file. Several potential files for each unit style are included
|
||||
in the ``potentials`` directory of the LAMMPS distribution.
|
||||
|
||||
Description
|
||||
"""""""""""
|
||||
|
||||
@ -46,15 +73,14 @@ The *oxdna/fene*, *oxdna2/fene*, and *oxrna2/fene* bond styles use the potential
|
||||
E = - \frac{\epsilon}{2} \ln \left[ 1 - \left(\frac{r-r_0}{\Delta}\right)^2\right]
|
||||
|
||||
to define a modified finite extensible nonlinear elastic (FENE)
|
||||
potential :ref:`(Ouldridge) <Ouldridge0>` to model the connectivity of the
|
||||
phosphate backbone in the oxDNA/oxRNA force field for coarse-grained
|
||||
potential :ref:`(Ouldridge) <Ouldridge0>` to model the connectivity of
|
||||
the phosphate backbone in the oxDNA/oxRNA force field for coarse-grained
|
||||
modelling of DNA/RNA.
|
||||
|
||||
The following coefficients must be defined for the bond type via the
|
||||
:doc:`bond_coeff <bond_coeff>` command as given in the above example, or
|
||||
in the data file or restart files read by the
|
||||
:doc:`read_data <read_data>` or :doc:`read_restart <read_restart>`
|
||||
commands:
|
||||
in the data file or restart files read by the :doc:`read_data
|
||||
<read_data>` or :doc:`read_restart <read_restart>` commands:
|
||||
|
||||
* :math:`\epsilon` (energy)
|
||||
* :math:`\Delta` (distance)
|
||||
@ -62,41 +88,40 @@ commands:
|
||||
|
||||
.. note::
|
||||
|
||||
The oxDNA bond style has to be used together with the
|
||||
corresponding oxDNA pair styles for excluded volume interaction
|
||||
*oxdna/excv* , stacking *oxdna/stk* , cross-stacking *oxdna/xstk* and
|
||||
coaxial stacking interaction *oxdna/coaxstk* as well as
|
||||
hydrogen-bonding interaction *oxdna/hbond* (see also documentation of
|
||||
:doc:`pair_style oxdna/excv <pair_oxdna>`). For the oxDNA2
|
||||
:ref:`(Snodin) <Snodin0>` bond style the analogous pair styles
|
||||
*oxdna2/excv* , *oxdna2/stk* , *oxdna2/xstk* , *oxdna2/coaxstk* ,
|
||||
*oxdna2/hbond* and an additional Debye-Hueckel pair style
|
||||
*oxdna2/dh* have to be defined. The same applies to the oxRNA2
|
||||
:ref:`(Sulc1) <Sulc01>` styles.
|
||||
The coefficients in the above example have to be kept fixed and cannot
|
||||
be changed without reparameterizing the entire model.
|
||||
The oxDNA bond style has to be used together with the corresponding
|
||||
oxDNA pair styles for excluded volume interaction *oxdna/excv* ,
|
||||
stacking *oxdna/stk* , cross-stacking *oxdna/xstk* and coaxial
|
||||
stacking interaction *oxdna/coaxstk* as well as hydrogen-bonding
|
||||
interaction *oxdna/hbond* (see also documentation of :doc:`pair_style
|
||||
oxdna/excv <pair_oxdna>`). For the oxDNA2 :ref:`(Snodin) <Snodin0>`
|
||||
bond style the analogous pair styles *oxdna2/excv* , *oxdna2/stk* ,
|
||||
*oxdna2/xstk* , *oxdna2/coaxstk* , *oxdna2/hbond* and an additional
|
||||
Debye-Hueckel pair style *oxdna2/dh* have to be defined. The same
|
||||
applies to the oxRNA2 :ref:`(Sulc1) <Sulc01>` styles.
|
||||
|
||||
.. note::
|
||||
|
||||
This bond style has to be used with the *atom_style hybrid bond ellipsoid oxdna*
|
||||
(see documentation of :doc:`atom_style <atom_style>`). The *atom_style oxdna*
|
||||
stores the 3'-to-5' polarity of the nucleotide strand, which is set through
|
||||
the bond topology in the data file. The first (second) atom in a bond definition
|
||||
is understood to point towards the 3'-end (5'-end) of the strand.
|
||||
This bond style has to be used with the *atom_style hybrid bond
|
||||
ellipsoid oxdna* (see documentation of :doc:`atom_style
|
||||
<atom_style>`). The *atom_style oxdna* stores the 3'-to-5' polarity
|
||||
of the nucleotide strand, which is set through the bond topology in
|
||||
the data file. The first (second) atom in a bond definition is
|
||||
understood to point towards the 3'-end (5'-end) of the strand.
|
||||
|
||||
.. warning::
|
||||
|
||||
If data files are produced with :doc:`write_data <write_data>`, then the
|
||||
:doc:`newton <newton>` command should be set to *newton on* or *newton off on*.
|
||||
Otherwise the data files will not have the same 3'-to-5' polarity as the
|
||||
initial data file. This limitation does not apply to binary restart files
|
||||
produced with :doc:`write_restart <write_restart>`.
|
||||
If data files are produced with :doc:`write_data <write_data>`, then
|
||||
the :doc:`newton <newton>` command should be set to *newton on* or
|
||||
*newton off on*. Otherwise the data files will not have the same
|
||||
3'-to-5' polarity as the initial data file. This limitation does not
|
||||
apply to binary restart files produced with :doc:`write_restart
|
||||
<write_restart>`.
|
||||
|
||||
Example input and data files for DNA and RNA duplexes can be found in
|
||||
examples/PACKAGES/cgdna/examples/oxDNA/ , /oxDNA2/ and /oxRNA2/. A simple python
|
||||
setup tool which creates single straight or helical DNA strands, DNA/RNA
|
||||
duplexes or arrays of DNA/RNA duplexes can be found in
|
||||
examples/PACKAGES/cgdna/util/.
|
||||
``examples/PACKAGES/cgdna/examples/oxDNA/`, `.../oxDNA2/`` and
|
||||
``.../oxRNA2/``. A simple python setup tool which creates single
|
||||
straight or helical DNA strands, DNA/RNA duplexes or arrays of DNA/RNA
|
||||
duplexes can be found in ``examples/PACKAGES/cgdna/util/``.
|
||||
|
||||
Please cite :ref:`(Henrich) <Henrich0>` in any publication that uses
|
||||
this implementation. An updated documentation that contains general information
|
||||
@ -113,6 +138,39 @@ and for sequence-specific hydrogen-bonding and stacking interactions
|
||||
|
||||
----------
|
||||
|
||||
Potential file reading
|
||||
""""""""""""""""""""""
|
||||
|
||||
For each style oxdna, oxdna2 and oxrna2, the first parameter argument
|
||||
can be a filename, and if it is, no further arguments should be
|
||||
supplied. Therefore the following command:
|
||||
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
bond_style oxdna/fene
|
||||
bond_coeff * oxdna_lj.cgdna
|
||||
|
||||
will be interpreted as a request to read the (FENE) potential
|
||||
:ref:`(Ouldridge) <Ouldridge0>` parameters from the file with the given
|
||||
name. The file can define multiple potential parameters for both bonded
|
||||
and pair interactions, but for the above bonded interactions there must
|
||||
exist in the file a line of the form:
|
||||
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
* fene epsilon delta r0
|
||||
|
||||
There are sample potential files for each unit style in the
|
||||
``potentials`` directory of the LAMMPS distribution. The potential file
|
||||
unit system must align with the units defined via the :doc:`units
|
||||
<units>` command. For conversion between different *LJ* and *real* unit
|
||||
systems for oxDNA, the python tool *lj2real.py* located in the
|
||||
``examples/PACKAGES/cgdna/util/`` directory can be used. This tool
|
||||
assumes similar file structure to the examples found in
|
||||
``examples/PACKAGES/cgdna/examples/``.
|
||||
|
||||
----------
|
||||
|
||||
Restrictions
|
||||
""""""""""""
|
||||
|
||||
|
||||
@ -37,18 +37,19 @@ Syntax
|
||||
|
||||
*oxdna/stk* args = seq T xi kappa 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
|
||||
seq = seqav (for average sequence stacking strength) or seqdep (for sequence-dependent stacking strength)
|
||||
T = temperature (oxDNA units, 0.1 = 300 K)
|
||||
xi = 1.3448 (temperature-independent coefficient in stacking strength)
|
||||
kappa = 2.6568 (coefficient of linear temperature dependence in stacking strength)
|
||||
T = temperature (LJ units: 0.1 = 300 K, real units: 300 = 300 K)
|
||||
xi = 1.3448 (LJ units) or 8.01727944817084 (real units), temperature-independent coefficient in stacking strength
|
||||
kappa = 2.6568 (LJ units) or 0.005279604 (real units), coefficient of linear temperature dependence in stacking strength
|
||||
*oxdna/hbond* args = seq eps 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
seq = seqav (for average sequence base-pairing strength) or seqdep (for sequence-dependent base-pairing strength)
|
||||
eps = 1.077 (between base pairs A-T and C-G) or 0 (all other pairs)
|
||||
eps = 1.077 (LJ units) or 6.42073911784652 (real units), average hydrogen bonding strength between A-T and C-G Watson-Crick base pairs, 0 between all other pairs
|
||||
|
||||
Examples
|
||||
""""""""
|
||||
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
# LJ units
|
||||
pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk
|
||||
pair_coeff * * oxdna/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
|
||||
pair_coeff * * oxdna/stk seqdep 0.1 1.3448 2.6568 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
|
||||
@ -58,55 +59,105 @@ Examples
|
||||
pair_coeff * * oxdna/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
|
||||
pair_coeff * * oxdna/coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 -0.65 2.0 -0.65
|
||||
|
||||
pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk
|
||||
pair_coeff * * oxdna/excv oxdna_lj.cgdna
|
||||
pair_coeff * * oxdna/stk seqav 0.1 1.3448 2.6568 oxdna_lj.cgdna
|
||||
pair_coeff * * oxdna/hbond seqav oxdna_lj.cgdna
|
||||
pair_coeff 1 4 oxdna/hbond seqav oxdna_lj.cgdna
|
||||
pair_coeff 2 3 oxdna/hbond seqav oxdna_lj.cgdna
|
||||
pair_coeff * * oxdna/xstk oxdna_lj.cgdna
|
||||
pair_coeff * * oxdna/coaxstk oxdna_lj.cgdna
|
||||
|
||||
# Real units
|
||||
pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk
|
||||
pair_coeff * * oxdna/excv 11.92337812042065 5.9626 5.74965 11.92337812042065 4.38677 4.259 11.92337812042065 2.81094 2.72576
|
||||
pair_coeff * * oxdna/stk seqdep 300.0 8.01727944817084 0.005279604 0.70439070204273 3.4072 7.6662 2.72576 6.3885 1.3 0.0 0.8 0.9 0.0 0.95 0.9 0.0 0.95 2.0 0.65 2.0 0.65
|
||||
pair_coeff * * oxdna/hbond seqdep 0.0 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0.0 0.7 1.5 0.0 0.7 1.5 0.0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45
|
||||
pair_coeff 1 4 oxdna/hbond seqdep 6.42073911784652 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0.0 0.7 1.5 0.0 0.7 1.5 0.0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45
|
||||
pair_coeff 2 3 oxdna/hbond seqdep 6.42073911784652 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0.0 0.7 1.5 0.0 0.7 1.5 0.0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45
|
||||
pair_coeff * * oxdna/xstk 3.9029021145006 4.89785 5.74965 4.21641 5.57929 2.25 0.791592654 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0.0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
|
||||
pair_coeff * * oxdna/coaxstk 3.77965257404268 3.4072 5.1108 1.87396 4.94044 2.0 2.541592654 0.65 1.3 0.0 0.8 0.9 0.0 0.95 0.9 0.0 0.95 2.0 -0.65 2.0 -0.65
|
||||
|
||||
pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk
|
||||
pair_coeff * * oxdna/excv oxdna_real.cgdna
|
||||
pair_coeff * * oxdna/stk seqav 300.0 8.01727944817084 0.005279604 oxdna_real.cgdna
|
||||
pair_coeff * * oxdna/hbond seqav oxdna_real.cgdna
|
||||
pair_coeff 1 4 oxdna/hbond seqav oxdna_real.cgdna
|
||||
pair_coeff 2 3 oxdna/hbond seqav oxdna_real.cgdna
|
||||
pair_coeff * * oxdna/xstk oxdna_real.cgdna
|
||||
pair_coeff * * oxdna/coaxstk oxdna_real.cgdna
|
||||
|
||||
.. note::
|
||||
|
||||
The coefficients in the above examples are provided in forms
|
||||
compatible with both *units lj* and *units real* (see documentation
|
||||
of :doc:`units <units>`). These can also be read from a potential
|
||||
file with correct unit style by specifying the name of the
|
||||
file. Several potential files for each unit style are included in the
|
||||
``potentials`` directory of the LAMMPS distribution.
|
||||
|
||||
Description
|
||||
"""""""""""
|
||||
|
||||
The *oxdna* pair styles compute the pairwise-additive parts of the oxDNA force field
|
||||
for coarse-grained modelling of DNA. The effective interaction between the nucleotides consists of potentials for the
|
||||
excluded volume interaction *oxdna/excv*, the stacking *oxdna/stk*, cross-stacking *oxdna/xstk*
|
||||
and coaxial stacking interaction *oxdna/coaxstk* as well
|
||||
as the hydrogen-bonding interaction *oxdna/hbond* between complementary pairs of nucleotides on
|
||||
opposite strands. Average sequence or sequence-dependent stacking and base-pairing strengths
|
||||
are supported :ref:`(Sulc) <Sulc1>`. Quasi-unique base-pairing between nucleotides can be achieved by using
|
||||
more complementary pairs of atom types like 5-8 and 6-7, 9-12 and 10-11, 13-16 and 14-15, etc.
|
||||
This prevents the hybridization of in principle complementary bases within Ntypes/4 bases
|
||||
up and down along the backbone.
|
||||
The *oxdna* pair styles compute the pairwise-additive parts of the oxDNA
|
||||
force field for coarse-grained modelling of DNA. The effective
|
||||
interaction between the nucleotides consists of potentials for the
|
||||
excluded volume interaction *oxdna/excv*, the stacking *oxdna/stk*,
|
||||
cross-stacking *oxdna/xstk* and coaxial stacking interaction
|
||||
*oxdna/coaxstk* as well as the hydrogen-bonding interaction
|
||||
*oxdna/hbond* between complementary pairs of nucleotides on opposite
|
||||
strands. Average sequence or sequence-dependent stacking and
|
||||
base-pairing strengths are supported :ref:`(Sulc) <Sulc1>`. Quasi-unique
|
||||
base-pairing between nucleotides can be achieved by using more
|
||||
complementary pairs of atom types like 5-8 and 6-7, 9-12 and 10-11,
|
||||
13-16 and 14-15, etc. This prevents the hybridization of in principle
|
||||
complementary bases within Ntypes/4 bases up and down along the
|
||||
backbone.
|
||||
|
||||
The exact functional form of the pair styles is rather complex.
|
||||
The individual potentials consist of products of modulation factors,
|
||||
which themselves are constructed from a number of more basic potentials
|
||||
(Morse, Lennard-Jones, harmonic angle and distance) as well as quadratic smoothing and modulation terms.
|
||||
We refer to :ref:`(Ouldridge-DPhil) <Ouldridge-DPhil1>` and :ref:`(Ouldridge) <Ouldridge1>`
|
||||
for a detailed description of the oxDNA force field.
|
||||
The exact functional form of the pair styles is rather complex. The
|
||||
individual potentials consist of products of modulation factors, which
|
||||
themselves are constructed from a number of more basic potentials
|
||||
(Morse, Lennard-Jones, harmonic angle and distance) as well as quadratic
|
||||
smoothing and modulation terms. We refer to :ref:`(Ouldridge-DPhil)
|
||||
<Ouldridge-DPhil1>` and :ref:`(Ouldridge) <Ouldridge1>` for a detailed
|
||||
description of the oxDNA force field.
|
||||
|
||||
.. note::
|
||||
|
||||
These pair styles have to be used together with the related oxDNA bond style
|
||||
*oxdna/fene* for the connectivity of the phosphate backbone (see also documentation of
|
||||
:doc:`bond_style oxdna/fene <bond_oxdna>`). Most of the coefficients
|
||||
in the above example have to be kept fixed and cannot be changed without reparameterizing the entire model.
|
||||
Exceptions are the first four coefficients after *oxdna/stk* (seq=seqdep, T=0.1, xi=1.3448 and kappa=2.6568 in the above example)
|
||||
and the first coefficient after *oxdna/hbond* (seq=seqdep in the above example).
|
||||
When using a Langevin thermostat, e.g. through :doc:`fix langevin <fix_langevin>`
|
||||
or :doc:`fix nve/dotc/langevin <fix_nve_dotc_langevin>`
|
||||
the temperature coefficients have to be matched to the one used in the fix.
|
||||
These pair styles have to be used together with the related oxDNA
|
||||
bond style *oxdna/fene* for the connectivity of the phosphate
|
||||
backbone (see also documentation of :doc:`bond_style oxdna/fene
|
||||
<bond_oxdna>`). Most of the coefficients in the above example have to
|
||||
be kept fixed and cannot be changed without reparameterizing the
|
||||
entire model. Exceptions are the first four coefficients after
|
||||
*oxdna/stk* (seq=seqdep, T=0.1, xi=1.3448 and kappa=2.6568 and
|
||||
corresponding *real unit* equivalents in the above examples) and the
|
||||
first coefficient after *oxdna/hbond* (seq=seqdep in the above
|
||||
example). When using a Langevin thermostat, e.g. through :doc:`fix
|
||||
langevin <fix_langevin>` or :doc:`fix nve/dotc/langevin
|
||||
<fix_nve_dotc_langevin>` the temperature coefficients have to be
|
||||
matched to the one used in the fix.
|
||||
|
||||
.. note::
|
||||
|
||||
These pair styles have to be used with the *atom_style hybrid bond ellipsoid oxdna*
|
||||
(see documentation of :doc:`atom_style <atom_style>`). The *atom_style oxdna*
|
||||
stores the 3'-to-5' polarity of the nucleotide strand, which is set through
|
||||
the bond topology in the data file. The first (second) atom in a bond definition
|
||||
is understood to point towards the 3'-end (5'-end) of the strand.
|
||||
These pair styles have to be used with the *atom_style hybrid bond
|
||||
ellipsoid oxdna* (see documentation of :doc:`atom_style
|
||||
<atom_style>`). The *atom_style oxdna* stores the 3'-to-5' polarity
|
||||
of the nucleotide strand, which is set through the bond topology in
|
||||
the data file. The first (second) atom in a bond definition is
|
||||
understood to point towards the 3'-end (5'-end) of the strand.
|
||||
|
||||
Example input and data files for DNA duplexes can be found in examples/PACKAGES/cgdna/examples/oxDNA/ and /oxDNA2/.
|
||||
A simple python setup tool which creates single straight or helical DNA strands,
|
||||
DNA duplexes or arrays of DNA duplexes can be found in examples/PACKAGES/cgdna/util/.
|
||||
Example input and data files for DNA duplexes can be found in
|
||||
``examples/PACKAGES/cgdna/examples/oxDNA/`` and ``.../oxDNA2/``. A
|
||||
simple python setup tool which creates single straight or helical DNA
|
||||
strands, DNA duplexes or arrays of DNA duplexes can be found in
|
||||
``examples/PACKAGES/cgdna/util/``.
|
||||
|
||||
Please cite :ref:`(Henrich) <Henrich1>` in any publication that uses
|
||||
this implementation. An updated documentation that contains general information
|
||||
on the model, its implementation and performance as well as the structure of
|
||||
the data and input file can be found `here <PDF/CG-DNA.pdf>`_.
|
||||
this implementation. An updated documentation that contains general
|
||||
information on the model, its implementation and performance as well as
|
||||
the structure of the data and input file can be found `here
|
||||
<PDF/CG-DNA.pdf>`_.
|
||||
|
||||
Please cite also the relevant oxDNA publications
|
||||
:ref:`(Ouldridge) <Ouldridge1>`,
|
||||
@ -115,6 +166,57 @@ and :ref:`(Sulc) <Sulc1>`.
|
||||
|
||||
----------
|
||||
|
||||
Potential file reading
|
||||
""""""""""""""""""""""
|
||||
|
||||
For each pair style above the first non-modifiable argument can be a
|
||||
filename, and if it is, no further arguments should be
|
||||
supplied. Therefore the following command:
|
||||
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
pair_coeff 1 4 oxdna/hbond seqav oxdna_lj.cgdna
|
||||
|
||||
will be interpreted as a request to read the corresponding hydrogen
|
||||
bonding potential parameters from the file with the given name. The file
|
||||
can define multiple potential parameters for both bonded and pair
|
||||
interactions, but for the example pair interaction above there must
|
||||
exist in the file a line of the form:
|
||||
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
1 4 hbond <coefficients>
|
||||
|
||||
If potential customization is required, the potential file reading can
|
||||
be mixed with the manual specification of the potential parameters. For
|
||||
example, the following command:
|
||||
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk
|
||||
pair_coeff * * oxdna/excv oxdna_lj.cgdna
|
||||
pair_coeff * * oxdna/stk seqav 0.1 1.3448 2.6568 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
|
||||
pair_coeff * * oxdna/hbond seqav oxdna_lj.cgdna
|
||||
pair_coeff 1 4 oxdna/hbond seqav oxdna_lj.cgdna
|
||||
pair_coeff 2 3 oxdna/hbond seqav oxdna_lj.cgdna
|
||||
pair_coeff * * oxdna/xstk oxdna_lj.cgdna
|
||||
pair_coeff * * oxdna/coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 -0.65 2.0 -0.65
|
||||
|
||||
will read the stacking and coaxial stacking potential parameters from
|
||||
the manual specification and all others from the potential file
|
||||
*oxdna_lj.cgdna*.
|
||||
|
||||
There are sample potential files for each unit style in the
|
||||
``potentials`` directory of the LAMMPS distribution. The potential file
|
||||
unit system must align with the units defined via the :doc:`units
|
||||
<units>` command. For conversion between different *LJ* and *real* unit
|
||||
systems for oxDNA, the python tool *lj2real.py* located in the
|
||||
``examples/PACKAGES/cgdna/util/`` directory can be used. This tool
|
||||
assumes similar file structure to the examples found in
|
||||
``examples/PACKAGES/cgdna/examples/``.
|
||||
|
||||
----------
|
||||
|
||||
Restrictions
|
||||
""""""""""""
|
||||
|
||||
|
||||
@ -41,14 +41,14 @@ Syntax
|
||||
|
||||
*oxdna2/stk* args = seq T xi kappa 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
|
||||
seq = seqav (for average sequence stacking strength) or seqdep (for sequence-dependent stacking strength)
|
||||
T = temperature (oxDNA units, 0.1 = 300 K)
|
||||
xi = 1.3523 (temperature-independent coefficient in stacking strength)
|
||||
kappa = 2.6717 (coefficient of linear temperature dependence in stacking strength)
|
||||
T = temperature (LJ units: 0.1 = 300 K, real units: 300 = 300 K)
|
||||
xi = 1.3523 (LJ units) or 8.06199211612242 (real units), temperature-independent coefficient in stacking strength
|
||||
kappa = 2.6717 (LJ units) or 0.005309213 (real units), coefficient of linear temperature dependence in stacking strength
|
||||
*oxdna2/hbond* args = seq eps 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
seq = seqav (for average sequence base-pairing strength) or seqdep (for sequence-dependent base-pairing strength)
|
||||
eps = 1.0678 (between base pairs A-T and C-G) or 0 (all other pairs)
|
||||
eps = 1.0678 (LJ units) or 6.36589157849259 (real units), average hydrogen bonding strength between A-T and C-G Watson-Crick base pairs, 0 between all other pairs
|
||||
*oxdna2/dh* args = T rhos qeff
|
||||
T = temperature (oxDNA units, 0.1 = 300 K)
|
||||
T = temperature (LJ units: 0.1 = 300 K, real units: 300 = 300 K)
|
||||
rhos = salt concentration (mole per litre)
|
||||
qeff = 0.815 (effective charge in elementary charges)
|
||||
|
||||
@ -57,6 +57,7 @@ Examples
|
||||
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
# LJ units
|
||||
pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
|
||||
pair_coeff * * oxdna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
|
||||
pair_coeff * * oxdna2/stk seqdep 0.1 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
|
||||
@ -67,61 +68,169 @@ Examples
|
||||
pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793
|
||||
pair_coeff * * oxdna2/dh 0.1 0.5 0.815
|
||||
|
||||
pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
|
||||
pair_coeff * * oxdna2/excv oxdna2_lj.cgdna
|
||||
pair_coeff * * oxdna2/stk seqdep 0.1 1.3523 2.6717 oxdna2_lj.cgdna
|
||||
pair_coeff * * oxdna2/hbond seqdep oxdna2_lj.cgdna
|
||||
pair_coeff 1 4 oxdna2/hbond seqdep oxdna2_lj.cgdna
|
||||
pair_coeff 2 3 oxdna2/hbond seqdep oxdna2_lj.cgdna
|
||||
pair_coeff * * oxdna2/xstk oxdna2_lj.cgdna
|
||||
pair_coeff * * oxdna2/coaxstk oxdna2_lj.cgdna
|
||||
pair_coeff * * oxdna2/dh 0.1 0.5 oxdna2_lj.cgdna
|
||||
|
||||
# Real units
|
||||
pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
|
||||
pair_coeff * * oxdna2/excv 11.92337812042065 5.9626 5.74965 11.92337812042065 4.38677 4.259 11.92337812042065 2.81094 2.72576
|
||||
pair_coeff * * oxdna2/stk seqdep 300.0 8.06199211612242 0.005309213 0.70439070204273 3.4072 7.6662 2.72576 6.3885 1.3 0.0 0.8 0.9 0.0 0.95 0.9 0.0 0.95 2.0 0.65 2.0 0.65
|
||||
pair_coeff * * oxdna2/hbond seqdep 0.0 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0.0 0.7 1.5 0.0 0.7 1.5 0.0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45
|
||||
pair_coeff 1 4 oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0.0 0.7 1.5 0.0 0.7 1.5 0.0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45
|
||||
pair_coeff 2 3 oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0.0 0.7 1.5 0.0 0.7 1.5 0.0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45
|
||||
pair_coeff * * oxdna2/xstk 3.9029021145006 4.89785 5.74965 4.21641 5.57929 2.25 0.791592654 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0.0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
|
||||
pair_coeff * * oxdna2/coaxstk 4.80673207785863 3.4072 5.1108 1.87396 4.94044 2.0 2.891592653589793 0.65 1.3 0.0 0.8 0.9 0.0 0.95 0.9 0.0 0.95 40.0 3.116592653589793
|
||||
pair_coeff * * oxdna2/dh 300.0 0.5 0.815
|
||||
|
||||
pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
|
||||
pair_coeff * * oxdna2/excv oxdna2_real.cgdna
|
||||
pair_coeff * * oxdna2/stk seqdep 300.0 8.06199211612242 0.005309213 oxdna2_real.cgdna
|
||||
pair_coeff * * oxdna2/hbond seqdep oxdna2_real.cgdna
|
||||
pair_coeff 1 4 oxdna2/hbond seqdep oxdna2_real.cgdna
|
||||
pair_coeff 2 3 oxdna2/hbond seqdep oxdna2_real.cgdna
|
||||
pair_coeff * * oxdna2/xstk oxdna2_real.cgdna
|
||||
pair_coeff * * oxdna2/coaxstk oxdna2_real.cgdna
|
||||
pair_coeff * * oxdna2/dh 300.0 0.5 oxdna2_real.cgdna
|
||||
|
||||
.. note::
|
||||
|
||||
The coefficients in the above examples are provided in forms
|
||||
compatible with both *units lj* and *units real* (see documentation
|
||||
of :doc:`units <units>`). These can also be read from a potential
|
||||
file with correct unit style by specifying the name of the
|
||||
file. Several potential files for each unit style are included in the
|
||||
``potentials`` directory of the LAMMPS distribution.
|
||||
|
||||
Description
|
||||
"""""""""""
|
||||
|
||||
The *oxdna2* pair styles compute the pairwise-additive parts of the oxDNA force field
|
||||
for coarse-grained modelling of DNA. The effective interaction between the nucleotides consists of potentials for the
|
||||
excluded volume interaction *oxdna2/excv*, the stacking *oxdna2/stk*, cross-stacking *oxdna2/xstk*
|
||||
and coaxial stacking interaction *oxdna2/coaxstk*, electrostatic Debye-Hueckel interaction *oxdna2/dh*
|
||||
as well as the hydrogen-bonding interaction *oxdna2/hbond* between complementary pairs of nucleotides on
|
||||
opposite strands. Average sequence or sequence-dependent stacking and base-pairing strengths
|
||||
are supported :ref:`(Sulc) <Sulc2>`. Quasi-unique base-pairing between nucleotides can be achieved by using
|
||||
more complementary pairs of atom types like 5-8 and 6-7, 9-12 and 10-11, 13-16 and 14-15, etc.
|
||||
This prevents the hybridization of in principle complementary bases within Ntypes/4 bases
|
||||
The *oxdna2* pair styles compute the pairwise-additive parts of the
|
||||
oxDNA force field for coarse-grained modelling of DNA. The effective
|
||||
interaction between the nucleotides consists of potentials for the
|
||||
excluded volume interaction *oxdna2/excv*, the stacking *oxdna2/stk*,
|
||||
cross-stacking *oxdna2/xstk* and coaxial stacking interaction
|
||||
*oxdna2/coaxstk*, electrostatic Debye-Hueckel interaction *oxdna2/dh* as
|
||||
well as the hydrogen-bonding interaction *oxdna2/hbond* between
|
||||
complementary pairs of nucleotides on opposite strands. Average sequence
|
||||
or sequence-dependent stacking and base-pairing strengths are supported
|
||||
:ref:`(Sulc) <Sulc2>`. Quasi-unique base-pairing between nucleotides can
|
||||
be achieved by using more complementary pairs of atom types like 5-8 and
|
||||
6-7, 9-12 and 10-11, 13-16 and 14-15, etc. This prevents the
|
||||
hybridization of in principle complementary bases within Ntypes/4 bases
|
||||
up and down along the backbone.
|
||||
|
||||
The exact functional form of the pair styles is rather complex.
|
||||
The individual potentials consist of products of modulation factors,
|
||||
which themselves are constructed from a number of more basic potentials
|
||||
(Morse, Lennard-Jones, harmonic angle and distance) as well as quadratic smoothing and modulation terms.
|
||||
We refer to :ref:`(Snodin) <Snodin2>` and the original oxDNA publications :ref:`(Ouldridge-DPhil) <Ouldridge-DPhil2>`
|
||||
and :ref:`(Ouldridge) <Ouldridge2>` for a detailed description of the oxDNA2 force field.
|
||||
The exact functional form of the pair styles is rather complex. The
|
||||
individual potentials consist of products of modulation factors, which
|
||||
themselves are constructed from a number of more basic potentials
|
||||
(Morse, Lennard-Jones, harmonic angle and distance) as well as quadratic
|
||||
smoothing and modulation terms. We refer to :ref:`(Snodin) <Snodin2>`
|
||||
and the original oxDNA publications :ref:`(Ouldridge-DPhil)
|
||||
<Ouldridge-DPhil2>` and :ref:`(Ouldridge) <Ouldridge2>` for a detailed
|
||||
description of the oxDNA2 force field.
|
||||
|
||||
.. note::
|
||||
|
||||
These pair styles have to be used together with the related oxDNA2 bond style
|
||||
*oxdna2/fene* for the connectivity of the phosphate backbone (see also documentation of
|
||||
:doc:`bond_style oxdna2/fene <bond_oxdna>`). Most of the coefficients
|
||||
in the above example have to be kept fixed and cannot be changed without reparameterizing the entire model.
|
||||
Exceptions are the first four coefficients after *oxdna2/stk* (seq=seqdep, T=0.1, xi=1.3523 and kappa=2.6717 in the above example),
|
||||
the first coefficient after *oxdna2/hbond* (seq=seqdep in the above example) and the three coefficients
|
||||
after *oxdna2/dh* (T=0.1, rhos=0.5, qeff=0.815 in the above example). When using a Langevin thermostat
|
||||
e.g. through :doc:`fix langevin <fix_langevin>` or :doc:`fix nve/dotc/langevin <fix_nve_dotc_langevin>`
|
||||
the temperature coefficients have to be matched to the one used in the fix.
|
||||
These pair styles have to be used together with the related oxDNA2
|
||||
bond style *oxdna2/fene* for the connectivity of the phosphate
|
||||
backbone (see also documentation of :doc:`bond_style oxdna2/fene
|
||||
<bond_oxdna>`). Most of the coefficients in the above example have to
|
||||
be kept fixed and cannot be changed without reparameterizing the
|
||||
entire model. Exceptions are the first four coefficients after
|
||||
*oxdna2/stk* (seq=seqdep, T=0.1, xi=1.3523 and kappa=2.6717 and
|
||||
corresponding *real unit* equivalents in the above examples). the
|
||||
first coefficient after *oxdna2/hbond* (seq=seqdep in the above
|
||||
example) and the three coefficients after *oxdna2/dh* (T=0.1,
|
||||
rhos=0.5, qeff=0.815 in the above example). When using a Langevin
|
||||
thermostat e.g. through :doc:`fix langevin <fix_langevin>` or
|
||||
:doc:`fix nve/dotc/langevin <fix_nve_dotc_langevin>` the temperature
|
||||
coefficients have to be matched to the one used in the fix.
|
||||
|
||||
.. note::
|
||||
|
||||
These pair styles have to be used with the *atom_style hybrid bond ellipsoid oxdna*
|
||||
(see documentation of :doc:`atom_style <atom_style>`). The *atom_style oxdna*
|
||||
stores the 3'-to-5' polarity of the nucleotide strand, which is set through
|
||||
the bond topology in the data file. The first (second) atom in a bond definition
|
||||
is understood to point towards the 3'-end (5'-end) of the strand.
|
||||
These pair styles have to be used with the *atom_style hybrid bond
|
||||
ellipsoid oxdna* (see documentation of :doc:`atom_style
|
||||
<atom_style>`). The *atom_style oxdna* stores the 3'-to-5' polarity
|
||||
of the nucleotide strand, which is set through the bond topology in
|
||||
the data file. The first (second) atom in a bond definition is
|
||||
understood to point towards the 3'-end (5'-end) of the strand.
|
||||
|
||||
Example input and data files for DNA duplexes can be found in examples/PACKAGES/cgdna/examples/oxDNA/ and /oxDNA2/.
|
||||
A simple python setup tool which creates single straight or helical DNA strands,
|
||||
DNA duplexes or arrays of DNA duplexes can be found in examples/PACKAGES/cgdna/util/.
|
||||
Example input and data files for DNA duplexes can be found in
|
||||
``examples/PACKAGES/cgdna/examples/oxDNA/`` and ``.../oxDNA2/``. A
|
||||
simple python setup tool which creates single straight or helical DNA
|
||||
strands, DNA duplexes or arrays of DNA duplexes can be found in
|
||||
``examples/PACKAGES/cgdna/util/``.
|
||||
|
||||
Please cite :ref:`(Henrich) <Henrich2>` in any publication that uses
|
||||
this implementation. An updated documentation that contains general information
|
||||
on the model, its implementation and performance as well as the structure of
|
||||
the data and input file can be found `here <PDF/CG-DNA.pdf>`_.
|
||||
this implementation. An updated documentation that contains general
|
||||
information on the model, its implementation and performance as well as
|
||||
the structure of the data and input file can be found `here
|
||||
<PDF/CG-DNA.pdf>`_.
|
||||
|
||||
Please cite also the relevant oxDNA2 publications
|
||||
:ref:`(Snodin) <Snodin2>` and :ref:`(Sulc) <Sulc2>`.
|
||||
|
||||
----------
|
||||
|
||||
Potential file reading
|
||||
""""""""""""""""""""""
|
||||
|
||||
For each pair style above the first non-modifiable argument can be a
|
||||
filename (with exception of Debye-Hueckel, for which the effective
|
||||
charge argument can be a filename), and if it is, no further arguments
|
||||
should be supplied. Therefore the following command:
|
||||
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
pair_coeff 1 4 oxdna2/hbond seqdep oxdna_real.cgdna
|
||||
|
||||
will be interpreted as a request to read the corresponding hydrogen
|
||||
bonding potential parameters from the file with the given name. The
|
||||
file can define multiple potential parameters for both bonded and pair
|
||||
interactions, but for the example pair interaction above there must
|
||||
exist in the file a line of the form:
|
||||
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
1 4 hbond <coefficients>
|
||||
|
||||
If potential customization is required, the potential file reading can
|
||||
be mixed with the manual specification of the potential parameters. For
|
||||
example, the following command:
|
||||
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
|
||||
pair_coeff * * oxdna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
|
||||
pair_coeff * * oxdna2/stk seqdep 0.1 1.3523 2.6717 oxdna2_lj.cgdna
|
||||
pair_coeff * * oxdna2/hbond seqdep oxdna2_lj.cgdna
|
||||
pair_coeff 1 4 oxdna2/hbond seqdep oxdna2_lj.cgdna
|
||||
pair_coeff 2 3 oxdna2/hbond seqdep oxdna2_lj.cgdna
|
||||
pair_coeff * * oxdna2/xstk oxdna2_lj.cgdna
|
||||
pair_coeff * * oxdna2/coaxstk oxdna2_lj.cgdna
|
||||
pair_coeff * * oxdna2/dh 0.1 0.5 0.815
|
||||
|
||||
will read the excluded volume and Debye-Hueckel effective charge *qeff*
|
||||
parameters from the manual specification and all others from the
|
||||
potential file *oxdna2_lj.cgdna*.
|
||||
|
||||
There are sample potential files for each unit style in the ``potentials``
|
||||
directory of the LAMMPS distribution. The potential file unit system
|
||||
must align with the units defined via the :doc:`units <units>`
|
||||
command. For conversion between different *LJ* and *real* unit systems
|
||||
for oxDNA, the python tool *lj2real.py* located in the
|
||||
``examples/PACKAGES/cgdna/util/`` directory can be used. This tool assumes
|
||||
similar file structure to the examples found in
|
||||
``examples/PACKAGES/cgdna/examples/``.
|
||||
|
||||
----------
|
||||
|
||||
Restrictions
|
||||
""""""""""""
|
||||
|
||||
|
||||
@ -41,14 +41,14 @@ Syntax
|
||||
|
||||
*oxrna2/stk* args = seq T xi kappa 6.0 0.43 0.93 0.35 0.78 0.9 0 0.95 0.9 0 0.95 1.3 0 0.8 1.3 0 0.8 2.0 0.65 2.0 0.65
|
||||
seq = seqav (for average sequence stacking strength) or seqdep (for sequence-dependent stacking strength)
|
||||
T = temperature (oxDNA units, 0.1 = 300 K)
|
||||
xi = 1.40206 (temperature-independent coefficient in stacking strength)
|
||||
kappa = 2.77 (coefficient of linear temperature dependence in stacking strength)
|
||||
T = temperature (LJ units: 0.1 = 300 K, real units: 300 = 300 K)
|
||||
xi = 1.40206 (LJ units) or 8.35864576375849 (real units), temperature-independent coefficient in stacking strength
|
||||
kappa = 2.77 (LJ units) or 0.005504556 (real units), coefficient of linear temperature dependence in stacking strength
|
||||
*oxrna2/hbond* args = seq eps 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
seq = seqav (for average sequence base-pairing strength) or seqdep (for sequence-dependent base-pairing strength)
|
||||
eps = 0.870439 (between base pairs A-T, C-G and G-T) or 0 (all other pairs)
|
||||
eps = 0.870439 (LJ units) or 5.18928666388042 (real units), average hydrogen bonding strength between A-U and C-G Watson-Crick and G-U wobble base pairs, 0 between all other pairs
|
||||
*oxrna2/dh* args = T rhos qeff
|
||||
T = temperature (oxDNA units, 0.1 = 300 K)
|
||||
T = temperature (LJ units: 0.1 = 300 K, real units: 300 = 300 K)
|
||||
rhos = salt concentration (mole per litre)
|
||||
qeff = 1.02455 (effective charge in elementary charges)
|
||||
|
||||
@ -57,6 +57,7 @@ Examples
|
||||
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
# LJ units
|
||||
pair_style hybrid/overlay oxrna2/excv oxrna2/stk oxrna2/hbond oxrna2/xstk oxrna2/coaxstk oxrna2/dh
|
||||
pair_coeff * * oxrna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
|
||||
pair_coeff * * oxrna2/stk seqdep 0.1 1.40206 2.77 6.0 0.43 0.93 0.35 0.78 0.9 0 0.95 0.9 0 0.95 1.3 0 0.8 1.3 0 0.8 2.0 0.65 2.0 0.65
|
||||
@ -68,58 +69,168 @@ Examples
|
||||
pair_coeff * * oxrna2/coaxstk 80 0.5 0.6 0.42 0.58 2.0 2.592 0.65 1.3 0.151 0.8 0.9 0.685 0.95 0.9 0.685 0.95 2.0 -0.65 2.0 -0.65
|
||||
pair_coeff * * oxrna2/dh 0.1 0.5 1.02455
|
||||
|
||||
pair_style hybrid/overlay oxrna2/excv oxrna2/stk oxrna2/hbond oxrna2/xstk oxrna2/coaxstk oxrna2/dh
|
||||
pair_coeff * * oxrna2/excv oxrna2_lj.cgdna
|
||||
pair_coeff * * oxrna2/stk seqdep 0.1 1.40206 2.77 oxrna2_lj.cgdna
|
||||
pair_coeff * * oxrna2/hbond seqdep oxrna2_lj.cgdna
|
||||
pair_coeff 1 4 oxrna2/hbond seqdep oxrna2_lj.cgdna
|
||||
pair_coeff 2 3 oxrna2/hbond seqdep oxrna2_lj.cgdna
|
||||
pair_coeff 3 4 oxrna2/hbond seqdep oxrna2_lj.cgdna
|
||||
pair_coeff * * oxrna2/xstk oxrna2_lj.cgdna
|
||||
pair_coeff * * oxrna2/coaxstk oxrna2_lj.cgdna
|
||||
pair_coeff * * oxrna2/dh 0.1 0.5 oxrna2_lj.cgdna
|
||||
|
||||
# Real units
|
||||
pair_style hybrid/overlay oxrna2/excv oxrna2/stk oxrna2/hbond oxrna2/xstk oxrna2/coaxstk oxrna2/dh
|
||||
pair_coeff * * oxrna2/excv 11.92337812042065 5.9626 5.74965 11.92337812042065 4.38677 4.259 11.92337812042065 2.81094 2.72576
|
||||
pair_coeff * * oxrna2/stk seqdep 300.0 8.35864576375849 0.005504556 0.70439070204273 3.66274 7.92174 2.9813 6.64404 0.9 0.0 0.95 0.9 0.0 0.95 1.3 0.0 0.8 1.3 0.0 0.8 2.0 0.65 2.0 0.65
|
||||
pair_coeff * * oxrna2/hbond seqdep 0.0 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0.0 0.7 1.5 0.0 0.7 1.5 0.0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 1 4 oxrna2/hbond seqdep 5.18928666388042 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0.0 0.7 1.5 0.0 0.7 1.5 0.0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 2 3 oxrna2/hbond seqdep 5.18928666388042 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0.0 0.7 1.5 0.0 0.7 1.5 0.0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 3 4 oxrna2/hbond seqdep 5.18928666388042 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0.0 0.7 1.5 0.0 0.7 1.5 0.0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff * * oxrna2/xstk 4.92690859644113 4.259 5.1108 3.57756 4.94044 2.25 0.505 0.58 1.7 1.266 0.68 1.7 1.266 0.68 1.7 0.309 0.68 1.7 0.309 0.68
|
||||
pair_coeff * * oxrna2/coaxstk 6.57330882442206 4.259 5.1108 3.57756 4.94044 2.0 2.592 0.65 1.3 0.151 0.8 0.9 0.685 0.95 0.9 0.685 0.95 2.0 -0.65 2.0 -0.65
|
||||
pair_coeff * * oxrna2/dh 300.0 0.5 1.02455
|
||||
|
||||
pair_style hybrid/overlay oxrna2/excv oxrna2/stk oxrna2/hbond oxrna2/xstk oxrna2/coaxstk oxrna2/dh
|
||||
pair_coeff * * oxrna2/excv oxrna2_real.cgdna
|
||||
pair_coeff * * oxrna2/stk seqdep 300.0 8.35864576375849 0.005504556 oxrna2_real.cgdna
|
||||
pair_coeff * * oxrna2/hbond seqdep oxrna2_real.cgdna
|
||||
pair_coeff 1 4 oxrna2/hbond seqdep oxrna2_real.cgdna
|
||||
pair_coeff 2 3 oxrna2/hbond seqdep oxrna2_real.cgdna
|
||||
pair_coeff 3 4 oxrna2/hbond seqdep oxrna2_real.cgdna
|
||||
pair_coeff * * oxrna2/xstk oxrna2_real.cgdna
|
||||
pair_coeff * * oxrna2/coaxstk oxrna2_real.cgdna
|
||||
pair_coeff * * oxrna2/dh 300.0 0.5 oxrna2_real.cgdna
|
||||
|
||||
.. note::
|
||||
|
||||
The coefficients in the above examples are provided in forms
|
||||
compatible with both *units lj* and *units real* (see documentation
|
||||
of :doc:`units <units>`). These can also be read from a potential
|
||||
file with correct unit style by specifying the name of the
|
||||
file. Several potential files for each unit style are included in the
|
||||
``potentials`` directory of the LAMMPS distribution.
|
||||
|
||||
Description
|
||||
"""""""""""
|
||||
|
||||
The *oxrna2* pair styles compute the pairwise-additive parts of the oxDNA force field
|
||||
for coarse-grained modelling of DNA. The effective interaction between the nucleotides consists of potentials for the
|
||||
excluded volume interaction *oxrna2/excv*, the stacking *oxrna2/stk*, cross-stacking *oxrna2/xstk*
|
||||
and coaxial stacking interaction *oxrna2/coaxstk*, electrostatic Debye-Hueckel interaction *oxrna2/dh*
|
||||
as well as the hydrogen-bonding interaction *oxrna2/hbond* between complementary pairs of nucleotides on
|
||||
opposite strands. Average sequence or sequence-dependent stacking and base-pairing strengths
|
||||
are supported :ref:`(Sulc2) <Sulc32>`. Quasi-unique base-pairing between nucleotides can be achieved by using
|
||||
more complementary pairs of atom types like 5-8 and 6-7, 9-12 and 10-11, 13-16 and 14-15, etc.
|
||||
This prevents the hybridization of in principle complementary bases within Ntypes/4 bases
|
||||
The *oxrna2* pair styles compute the pairwise-additive parts of the
|
||||
oxDNA force field for coarse-grained modelling of RNA. The effective
|
||||
interaction between the nucleotides consists of potentials for the
|
||||
excluded volume interaction *oxrna2/excv*, the stacking *oxrna2/stk*,
|
||||
cross-stacking *oxrna2/xstk* and coaxial stacking interaction
|
||||
*oxrna2/coaxstk*, electrostatic Debye-Hueckel interaction *oxrna2/dh* as
|
||||
well as the hydrogen-bonding interaction *oxrna2/hbond* between
|
||||
complementary pairs of nucleotides on opposite strands. Average sequence
|
||||
or sequence-dependent stacking and base-pairing strengths are supported
|
||||
:ref:`(Sulc2) <Sulc32>`. Quasi-unique base-pairing between nucleotides
|
||||
can be achieved by using more complementary pairs of atom types like 5-8
|
||||
and 6-7, 9-12 and 10-11, 13-16 and 14-15, etc. This prevents the
|
||||
hybridization of in principle complementary bases within Ntypes/4 bases
|
||||
up and down along the backbone.
|
||||
|
||||
The exact functional form of the pair styles is rather complex.
|
||||
The individual potentials consist of products of modulation factors,
|
||||
which themselves are constructed from a number of more basic potentials
|
||||
(Morse, Lennard-Jones, harmonic angle and distance) as well as quadratic smoothing and modulation terms.
|
||||
We refer to :ref:`(Sulc1) <Sulc31>` and the original oxDNA publications :ref:`(Ouldridge-DPhil) <Ouldridge-DPhil3>`
|
||||
and :ref:`(Ouldridge) <Ouldridge3>` for a detailed description of the oxRNA2 force field.
|
||||
The exact functional form of the pair styles is rather complex. The
|
||||
individual potentials consist of products of modulation factors, which
|
||||
themselves are constructed from a number of more basic potentials
|
||||
(Morse, Lennard-Jones, harmonic angle and distance) as well as quadratic
|
||||
smoothing and modulation terms. We refer to :ref:`(Sulc1) <Sulc31>` and
|
||||
the original oxDNA publications :ref:`(Ouldridge-DPhil)
|
||||
<Ouldridge-DPhil3>` and :ref:`(Ouldridge) <Ouldridge3>` for a detailed
|
||||
description of the oxRNA2 force field.
|
||||
|
||||
.. note::
|
||||
|
||||
These pair styles have to be used together with the related oxDNA2 bond style
|
||||
*oxrna2/fene* for the connectivity of the phosphate backbone (see also documentation of
|
||||
:doc:`bond_style oxrna2/fene <bond_oxdna>`). Most of the coefficients
|
||||
in the above example have to be kept fixed and cannot be changed without reparameterizing the entire model.
|
||||
Exceptions are the first four coefficients after *oxrna2/stk* (seq=seqdep, T=0.1, xi=1.40206 and kappa=2.77 in the above example),
|
||||
the first coefficient after *oxrna2/hbond* (seq=seqdep in the above example) and the three coefficients
|
||||
after *oxrna2/dh* (T=0.1, rhos=0.5, qeff=1.02455 in the above example). When using a Langevin thermostat
|
||||
e.g. through :doc:`fix langevin <fix_langevin>` or :doc:`fix nve/dotc/langevin <fix_nve_dotc_langevin>`
|
||||
the temperature coefficients have to be matched to the one used in the fix.
|
||||
These pair styles have to be used together with the related oxDNA2
|
||||
bond style *oxrna2/fene* for the connectivity of the phosphate
|
||||
backbone (see also documentation of :doc:`bond_style oxrna2/fene
|
||||
<bond_oxdna>`). Most of the coefficients in the above example have to
|
||||
be kept fixed and cannot be changed without reparameterizing the
|
||||
entire model. Exceptions are the first four coefficients after
|
||||
*oxrna2/stk* (seq=seqdep, T=0.1, xi=1.40206 and kappa=2.77 and
|
||||
corresponding *real unit* equivalents in the above examples), the
|
||||
first coefficient after *oxrna2/hbond* (seq=seqdep in the above
|
||||
example) and the three coefficients after *oxrna2/dh* (T=0.1,
|
||||
rhos=0.5, qeff=1.02455 in the above example). When using a Langevin
|
||||
thermostat e.g. through :doc:`fix langevin <fix_langevin>` or
|
||||
:doc:`fix nve/dotc/langevin <fix_nve_dotc_langevin>` the temperature
|
||||
coefficients have to be matched to the one used in the fix.
|
||||
|
||||
.. note::
|
||||
|
||||
These pair styles have to be used with the *atom_style hybrid bond ellipsoid oxdna*
|
||||
(see documentation of :doc:`atom_style <atom_style>`). The *atom_style oxdna*
|
||||
stores the 3'-to-5' polarity of the nucleotide strand, which is set through
|
||||
the bond topology in the data file. The first (second) atom in a bond definition
|
||||
is understood to point towards the 3'-end (5'-end) of the strand.
|
||||
These pair styles have to be used with the *atom_style hybrid bond
|
||||
ellipsoid oxdna* (see documentation of :doc:`atom_style
|
||||
<atom_style>`). The *atom_style oxdna* stores the 3'-to-5' polarity
|
||||
of the nucleotide strand, which is set through the bond topology in
|
||||
the data file. The first (second) atom in a bond definition is
|
||||
understood to point towards the 3'-end (5'-end) of the strand.
|
||||
|
||||
Example input and data files for DNA duplexes can be found in examples/PACKAGES/cgdna/examples/oxDNA/ and /oxDNA2/.
|
||||
A simple python setup tool which creates single straight or helical DNA strands,
|
||||
DNA duplexes or arrays of DNA duplexes can be found in examples/PACKAGES/cgdna/util/.
|
||||
Example input and data files for DNA duplexes can be found in
|
||||
``examples/PACKAGES/cgdna/examples/oxDNA/`` and ``.../oxDNA2/``. A simple python
|
||||
setup tool which creates single straight or helical DNA strands, DNA
|
||||
duplexes or arrays of DNA duplexes can be found in
|
||||
``examples/PACKAGES/cgdna/util/``.
|
||||
|
||||
Please cite :ref:`(Henrich) <Henrich3>` in any publication that uses
|
||||
this implementation. The article contains general information
|
||||
on the model, its implementation and performance as well as the structure of
|
||||
the data and input file. The preprint version of the article can be found
|
||||
`here <PDF/CG-DNA.pdf>`_.
|
||||
Please cite also the relevant oxRNA2 publications
|
||||
:ref:`(Sulc1) <Sulc31>` and :ref:`(Sulc2) <Sulc32>`.
|
||||
this implementation. The article contains general information on the
|
||||
model, its implementation and performance as well as the structure of
|
||||
the data and input file. The preprint version of the article can be
|
||||
found `here <PDF/CG-DNA.pdf>`_. Please cite also the relevant oxRNA2
|
||||
publications :ref:`(Sulc1) <Sulc31>` and :ref:`(Sulc2) <Sulc32>`.
|
||||
|
||||
----------
|
||||
|
||||
Potential file reading
|
||||
""""""""""""""""""""""
|
||||
|
||||
For each pair style above the first non-modifiable argument can be a
|
||||
filename (with exception of Debye-Hueckel, for which the effective
|
||||
charge argument can be a filename), and if it is, no further arguments
|
||||
should be supplied. Therefore the following command:
|
||||
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
pair_coeff 3 4 oxrna2/hbond seqdep oxrna2_lj.cgdna
|
||||
|
||||
will be interpreted as a request to read the corresponding hydrogen
|
||||
bonding potential parameters from the file with the given name. The
|
||||
file can define multiple potential parameters for both bonded and pair
|
||||
interactions, but for the example pair interaction above there must
|
||||
exist in the file a line of the form:
|
||||
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
3 4 hbond <coefficients>
|
||||
|
||||
If potential customization is required, the potential file reading can
|
||||
be mixed with the manual specification of the potential parameters. For
|
||||
example, the following command:
|
||||
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
pair_style hybrid/overlay oxrna2/excv oxrna2/stk oxrna2/hbond oxrna2/xstk oxrna2/coaxstk oxrna2/dh
|
||||
pair_coeff * * oxrna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
|
||||
pair_coeff * * oxrna2/stk seqdep 0.1 1.40206 2.77 oxrna2_lj.cgdna
|
||||
pair_coeff * * oxrna2/hbond seqdep oxrna2_lj.cgdna
|
||||
pair_coeff 1 4 oxrna2/hbond seqdep oxrna2_lj.cgdna
|
||||
pair_coeff 2 3 oxrna2/hbond seqdep oxrna2_lj.cgdna
|
||||
pair_coeff 3 4 oxrna2/hbond seqdep oxrna2_lj.cgdna
|
||||
pair_coeff * * oxrna2/xstk oxrna2_lj.cgdna
|
||||
pair_coeff * * oxrna2/coaxstk oxrna2_lj.cgdna
|
||||
pair_coeff * * oxrna2/dh 0.1 0.5 1.02455
|
||||
|
||||
will read the excluded volume and Debye-Hueckel effective charge *qeff*
|
||||
parameters from the manual specification and all others from the
|
||||
potential file *oxrna2_lj.cgdna*.
|
||||
|
||||
There are sample potential files for each unit style in the
|
||||
``potentials`` directory of the LAMMPS distribution. The potential file
|
||||
unit system must align with the units defined via the :doc:`units
|
||||
<units>` command. For conversion between different *LJ* and *real* unit
|
||||
systems for oxDNA, the python tool *lj2real.py* located in the
|
||||
``examples/PACKAGES/cgdna/util/`` directory can be used. This tool
|
||||
assumes similar file structure to the examples found in
|
||||
``examples/PACKAGES/cgdna/examples/``.
|
||||
|
||||
----------
|
||||
|
||||
|
||||
@ -0,0 +1,70 @@
|
||||
variable number equal 1
|
||||
variable ofreq equal 1000
|
||||
variable efreq equal 1000
|
||||
variable T equal 0.1
|
||||
|
||||
units lj
|
||||
|
||||
dimension 3
|
||||
|
||||
newton on
|
||||
|
||||
boundary p p p
|
||||
|
||||
atom_style hybrid bond ellipsoid oxdna
|
||||
atom_modify sort 0 1.0
|
||||
|
||||
# Pair interactions require lists of neighbours to be calculated
|
||||
neighbor 2.0 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
read_data data.duplex1
|
||||
|
||||
set atom * mass 3.1575
|
||||
|
||||
group all type 1 4
|
||||
|
||||
# oxDNA bond interactions - FENE backbone
|
||||
bond_style oxdna/fene
|
||||
bond_coeff * oxdna_lj.cgdna
|
||||
special_bonds lj 0 1 1
|
||||
|
||||
# oxDNA pair interactions
|
||||
pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk
|
||||
pair_coeff * * oxdna/excv oxdna_lj.cgdna
|
||||
pair_coeff * * oxdna/stk seqav 0.1 1.3448 2.6568 oxdna_lj.cgdna
|
||||
pair_coeff * * oxdna/hbond seqav oxdna_lj.cgdna
|
||||
pair_coeff 1 4 oxdna/hbond seqav oxdna_lj.cgdna
|
||||
pair_coeff 2 3 oxdna/hbond seqav oxdna_lj.cgdna
|
||||
pair_coeff * * oxdna/xstk oxdna_lj.cgdna
|
||||
pair_coeff * * oxdna/coaxstk oxdna_lj.cgdna
|
||||
|
||||
# NVE ensemble
|
||||
fix 1 all nve/asphere
|
||||
#fix 2 all langevin ${T} ${T} 2.5 457145 angmom 10
|
||||
|
||||
timestep 1e-5
|
||||
|
||||
#comm_style tiled
|
||||
fix 3 all balance 1000 1.03 shift xyz 10 1.03
|
||||
comm_modify cutoff 3.8
|
||||
|
||||
compute quat all property/atom quatw quati quatj quatk
|
||||
|
||||
compute erot all erotate/asphere
|
||||
compute ekin all ke
|
||||
compute epot all pe
|
||||
variable erot equal c_erot
|
||||
variable ekin equal c_ekin
|
||||
variable epot equal c_epot
|
||||
variable etot equal c_erot+c_ekin+c_epot
|
||||
fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
|
||||
|
||||
dump out all custom ${ofreq} out.${number}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz
|
||||
dump_modify out sort id
|
||||
dump_modify out format line "%d %d %d %22.15le %22.15le %22.15le %d %d %d %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le"
|
||||
|
||||
run 1000000
|
||||
|
||||
write_data last_config.${number}.* nocoeff
|
||||
#write_restart last_config.${number}.*
|
||||
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
@ -0,0 +1 @@
|
||||
../../../../../../../potentials/oxdna_lj.cgdna
|
||||
@ -0,0 +1,68 @@
|
||||
LAMMPS data file via write_data, version 27 May 2021
|
||||
|
||||
10 atoms
|
||||
4 atom types
|
||||
8 bonds
|
||||
1 bond types
|
||||
10 ellipsoids
|
||||
|
||||
-20 20 xlo xhi
|
||||
-20 20 ylo yhi
|
||||
-20 20 zlo zhi
|
||||
|
||||
Masses
|
||||
|
||||
1 3.1575
|
||||
2 3.1575
|
||||
3 3.1575
|
||||
4 3.1575
|
||||
|
||||
Atoms # hybrid
|
||||
|
||||
1 1 -0.33741452300167507 -0.43708835412476305 0.6450685042019271 1 1 3.7269849963023267 0 0 0
|
||||
2 2 -0.32142606102826937 -0.7137743037592722 1.1817366147004618 1 1 3.7269849963023267 0 0 0
|
||||
3 3 -0.130363628207774 -0.9147144801536078 1.62581312195109 1 1 3.7269849963023267 0 0 0
|
||||
4 4 0.16795127962282844 -0.9808507459807022 2.0894908590909003 1 1 3.7269849963023267 0 0 0
|
||||
5 1 0.46370423490634166 -0.7803347954883079 2.4251986815515827 1 1 3.7269849963023267 0 0 0
|
||||
6 4 -0.4462950185476711 0.09062163051035639 2.4668941268777607 2 1 3.7269849963023267 0 0 0
|
||||
7 1 -0.03377054097560965 0.20979847489755046 2.078208732038921 2 1 3.7269849963023267 0 0 0
|
||||
8 2 0.3297325391466579 0.17657587120899895 1.7206328374934152 2 1 3.7269849963023267 0 0 0
|
||||
9 3 0.6063699309305985 0.04682595158675571 1.2335049647817748 2 1 3.7269849963023267 0 0 0
|
||||
10 4 0.8003979559814726 -0.364393011459011 0.9884025318908612 2 1 3.7269849963023267 0 0 0
|
||||
|
||||
Velocities
|
||||
|
||||
1 0.320321385294804 -0.13632815939410442 -0.029398292452023418 0.3064009492028237 -0.15808560233691588 0.35878007201886397
|
||||
2 0.16868594667473025 -0.04950805613064363 0.15811007290373785 -0.07666583909321756 -0.0008074676325318194 -0.21475821019816385
|
||||
3 -0.22924557018300165 0.08381876748892438 -0.0919832851533896 0.4039387481683193 0.6123610642545824 -0.11063432848545783
|
||||
4 -0.22186204313310393 0.04952817499985707 -0.0693642101605732 -0.1358248430264938 0.4118493572385653 -0.056529305922687775
|
||||
5 0.08156431270087049 -0.2564594759800144 0.1724544416027875 0.05439894663158808 0.09338481510384318 0.3205408219238883
|
||||
6 0.03598698404367743 -0.04868642973674152 0.02860105256592922 0.04007709957283992 -0.317943400069374 0.36438025397586354
|
||||
7 -0.00822868972307372 0.047514932936351305 -0.027726409420297023 0.18356392696891796 -0.49877294396308003 0.06993313839189567
|
||||
8 -0.07177147672242379 0.1718272727853115 0.39056151182616994 -0.16728362538690794 -0.47839708820957955 -0.17897249005947627
|
||||
9 -0.1748638855727651 -0.0781638161351808 0.0560181565271157 -0.28062568580131014 0.2405396522734162 -0.4311598357169048
|
||||
10 0.18870318272756448 -0.1066780134639517 0.12610657946741227 -0.05740397100183697 0.36748833227892685 0.1498775724372025
|
||||
|
||||
Bonds
|
||||
|
||||
1 1 1 2
|
||||
2 1 2 3
|
||||
3 1 3 4
|
||||
4 1 4 5
|
||||
5 1 6 7
|
||||
6 1 7 8
|
||||
7 1 8 9
|
||||
8 1 9 10
|
||||
|
||||
Ellipsoids
|
||||
|
||||
1 1.173984503142341 1.173984503142341 1.173984503142341 0.9890278201757743 0.01779228232037064 -0.14337734159225404 0.030827642240801516
|
||||
2 1.173984503142341 1.173984503142341 1.173984503142341 0.939687458852748 0.04174166924055095 -0.023337773785056866 0.338674565089608
|
||||
3 1.173984503142341 1.173984503142341 1.173984503142341 0.8210113150655425 0.03012140921736572 0.017666019956944813 0.5698429897612057
|
||||
4 1.173984503142341 1.173984503142341 1.173984503142341 0.6623662858285051 -0.028186343967346823 0.022942552517501488 0.7482981175276918
|
||||
5 1.173984503142341 1.173984503142341 1.173984503142341 0.3601488726765216 0.0513614985821682 0.0724224158335286 0.9286602067807472
|
||||
6 1.173984503142341 1.173984503142341 1.173984503142341 0.11941234710084649 0.9244660117493703 -0.35317942248051865 -0.07979711784524246
|
||||
7 1.173984503142341 1.173984503142341 1.173984503142341 -0.17949125421205164 0.7412884899431119 -0.6379094464220707 0.1065166771202199
|
||||
8 1.173984503142341 1.173984503142341 1.173984503142341 -0.10483691088405202 0.5508895999584645 -0.8250090480220789 0.06992811634525403
|
||||
9 1.173984503142341 1.173984503142341 1.173984503142341 0.07777239911646 -0.3724087549185288 0.9103052384821374 -0.1631181963720798
|
||||
10 1.173984503142341 1.173984503142341 1.173984503142341 0.16279109707978262 0.027148630125149613 0.9849325709665359 -0.0516705065113425
|
||||
@ -0,0 +1,68 @@
|
||||
LAMMPS data file via write_data, version 27 May 2021
|
||||
|
||||
10 atoms
|
||||
4 atom types
|
||||
8 bonds
|
||||
1 bond types
|
||||
10 ellipsoids
|
||||
|
||||
-20 20 xlo xhi
|
||||
-20 20 ylo yhi
|
||||
-20 20 zlo zhi
|
||||
|
||||
Masses
|
||||
|
||||
1 3.1575
|
||||
2 3.1575
|
||||
3 3.1575
|
||||
4 3.1575
|
||||
|
||||
Atoms # hybrid
|
||||
|
||||
1 1 -0.33741452300167507 -0.43708835412476305 0.6450685042019271 1 1 3.7269849963023267 0 0 0
|
||||
2 2 -0.32142606102826937 -0.7137743037592722 1.1817366147004618 1 1 3.7269849963023267 0 0 0
|
||||
3 3 -0.130363628207774 -0.9147144801536078 1.62581312195109 1 1 3.7269849963023267 0 0 0
|
||||
4 4 0.16795127962282844 -0.9808507459807022 2.0894908590909003 1 1 3.7269849963023267 0 0 0
|
||||
5 1 0.46370423490634166 -0.7803347954883079 2.4251986815515827 1 1 3.7269849963023267 0 0 0
|
||||
6 4 -0.4462950185476711 0.09062163051035639 2.4668941268777607 2 1 3.7269849963023267 0 0 0
|
||||
7 1 -0.03377054097560965 0.20979847489755046 2.078208732038921 2 1 3.7269849963023267 0 0 0
|
||||
8 2 0.3297325391466579 0.17657587120899895 1.7206328374934152 2 1 3.7269849963023267 0 0 0
|
||||
9 3 0.6063699309305985 0.04682595158675571 1.2335049647817748 2 1 3.7269849963023267 0 0 0
|
||||
10 4 0.8003979559814726 -0.364393011459011 0.9884025318908612 2 1 3.7269849963023267 0 0 0
|
||||
|
||||
Velocities
|
||||
|
||||
1 0.320321385294804 -0.13632815939410442 -0.029398292452023418 0.3064009492028237 -0.15808560233691588 0.35878007201886397
|
||||
2 0.16868594667473025 -0.04950805613064363 0.15811007290373785 -0.07666583909321756 -0.0008074676325318194 -0.21475821019816385
|
||||
3 -0.22924557018300165 0.08381876748892438 -0.0919832851533896 0.4039387481683193 0.6123610642545824 -0.11063432848545783
|
||||
4 -0.22186204313310393 0.04952817499985707 -0.0693642101605732 -0.1358248430264938 0.4118493572385653 -0.056529305922687775
|
||||
5 0.08156431270087049 -0.2564594759800144 0.1724544416027875 0.05439894663158808 0.09338481510384318 0.3205408219238883
|
||||
6 0.03598698404367743 -0.04868642973674152 0.02860105256592922 0.04007709957283992 -0.317943400069374 0.36438025397586354
|
||||
7 -0.00822868972307372 0.047514932936351305 -0.027726409420297023 0.18356392696891796 -0.49877294396308003 0.06993313839189567
|
||||
8 -0.07177147672242379 0.1718272727853115 0.39056151182616994 -0.16728362538690794 -0.47839708820957955 -0.17897249005947627
|
||||
9 -0.1748638855727651 -0.0781638161351808 0.0560181565271157 -0.28062568580131014 0.2405396522734162 -0.4311598357169048
|
||||
10 0.18870318272756448 -0.1066780134639517 0.12610657946741227 -0.05740397100183697 0.36748833227892685 0.1498775724372025
|
||||
|
||||
Bonds
|
||||
|
||||
1 1 1 2
|
||||
2 1 2 3
|
||||
3 1 3 4
|
||||
4 1 4 5
|
||||
5 1 6 7
|
||||
6 1 7 8
|
||||
7 1 8 9
|
||||
8 1 9 10
|
||||
|
||||
Ellipsoids
|
||||
|
||||
1 1.173984503142341 1.173984503142341 1.173984503142341 0.9890278201757743 0.01779228232037064 -0.14337734159225404 0.030827642240801516
|
||||
2 1.173984503142341 1.173984503142341 1.173984503142341 0.939687458852748 0.04174166924055095 -0.023337773785056866 0.338674565089608
|
||||
3 1.173984503142341 1.173984503142341 1.173984503142341 0.8210113150655425 0.03012140921736572 0.017666019956944813 0.5698429897612057
|
||||
4 1.173984503142341 1.173984503142341 1.173984503142341 0.6623662858285051 -0.028186343967346823 0.022942552517501488 0.7482981175276918
|
||||
5 1.173984503142341 1.173984503142341 1.173984503142341 0.3601488726765216 0.0513614985821682 0.0724224158335286 0.9286602067807472
|
||||
6 1.173984503142341 1.173984503142341 1.173984503142341 0.11941234710084649 0.9244660117493703 -0.35317942248051865 -0.07979711784524246
|
||||
7 1.173984503142341 1.173984503142341 1.173984503142341 -0.17949125421205164 0.7412884899431119 -0.6379094464220707 0.1065166771202199
|
||||
8 1.173984503142341 1.173984503142341 1.173984503142341 -0.10483691088405202 0.5508895999584645 -0.8250090480220789 0.06992811634525403
|
||||
9 1.173984503142341 1.173984503142341 1.173984503142341 0.07777239911646 -0.3724087549185288 0.9103052384821374 -0.1631181963720798
|
||||
10 1.173984503142341 1.173984503142341 1.173984503142341 0.16279109707978262 0.027148630125149613 0.9849325709665359 -0.0516705065113425
|
||||
@ -0,0 +1,72 @@
|
||||
variable number equal 1
|
||||
variable ofreq equal 1000
|
||||
variable efreq equal 1000
|
||||
variable T equal 0.1
|
||||
variable rhos equal 0.2
|
||||
|
||||
units lj
|
||||
|
||||
dimension 3
|
||||
|
||||
newton on
|
||||
|
||||
boundary p p p
|
||||
|
||||
atom_style hybrid bond ellipsoid oxdna
|
||||
atom_modify sort 0 1.0
|
||||
|
||||
# Pair interactions require lists of neighbours to be calculated
|
||||
neighbor 2.0 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
read_data data.duplex1
|
||||
|
||||
set atom * mass 3.1575
|
||||
|
||||
group all type 1 4
|
||||
|
||||
# oxDNA2 bond interactions - FENE backbone
|
||||
bond_style oxdna2/fene
|
||||
bond_coeff * oxdna2_lj.cgdna
|
||||
special_bonds lj 0 1 1
|
||||
|
||||
# oxDNA2 pair interactions
|
||||
pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
|
||||
pair_coeff * * oxdna2/excv oxdna2_lj.cgdna
|
||||
pair_coeff * * oxdna2/stk seqdep 0.1 1.3523 2.6717 oxdna2_lj.cgdna
|
||||
pair_coeff * * oxdna2/hbond seqdep oxdna2_lj.cgdna
|
||||
pair_coeff 1 4 oxdna2/hbond seqdep oxdna2_lj.cgdna
|
||||
pair_coeff 2 3 oxdna2/hbond seqdep oxdna2_lj.cgdna
|
||||
pair_coeff * * oxdna2/xstk oxdna2_lj.cgdna
|
||||
pair_coeff * * oxdna2/coaxstk oxdna2_lj.cgdna
|
||||
pair_coeff * * oxdna2/dh 0.1 0.5 oxdna2_lj.cgdna
|
||||
|
||||
# NVE ensemble
|
||||
fix 1 all nve/asphere
|
||||
#fix 2 all langevin ${T} ${T} 2.5 457145 angmom 10
|
||||
|
||||
timestep 1e-5
|
||||
|
||||
#comm_style tiled
|
||||
fix 3 all balance 1000 1.03 shift xyz 10 1.03
|
||||
comm_modify cutoff 3.8
|
||||
|
||||
compute quat all property/atom quatw quati quatj quatk
|
||||
|
||||
compute erot all erotate/asphere
|
||||
compute ekin all ke
|
||||
compute epot all pe
|
||||
variable erot equal c_erot
|
||||
variable ekin equal c_ekin
|
||||
variable epot equal c_epot
|
||||
variable etot equal c_erot+c_ekin+c_epot
|
||||
fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
|
||||
|
||||
dump out all custom ${ofreq} out.${number}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz
|
||||
dump_modify out sort id
|
||||
dump_modify out format line "%d %d %d %22.15le %22.15le %22.15le %d %d %d %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le"
|
||||
|
||||
run 1000000
|
||||
|
||||
write_data last_config.${number}.* nocoeff
|
||||
#write_restart last_config.${number}.*
|
||||
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
@ -0,0 +1 @@
|
||||
../../../../../../../potentials/oxdna2_lj.cgdna
|
||||
@ -0,0 +1,91 @@
|
||||
LAMMPS data file via write_data, version 27 May 2021
|
||||
|
||||
16 atoms
|
||||
4 atom types
|
||||
13 bonds
|
||||
1 bond types
|
||||
16 ellipsoids
|
||||
|
||||
-20 20 xlo xhi
|
||||
-20 20 ylo yhi
|
||||
-20 20 zlo zhi
|
||||
|
||||
Masses
|
||||
|
||||
1 3.1575
|
||||
2 3.1575
|
||||
3 3.1575
|
||||
4 3.1575
|
||||
|
||||
Atoms # hybrid
|
||||
|
||||
1 1 -0.6133472972454725 -0.657478171669766 0.36065226351201896 1 1 3.7269849963023267 0 0 0
|
||||
2 2 -0.45262764247356363 -1.0030650534345913 0.7258693379233347 1 1 3.7269849963023267 0 0 0
|
||||
3 3 -0.0988342108522641 -1.239775807128057 1.069462285786363 1 1 3.7269849963023267 0 0 0
|
||||
4 4 0.2937771854299732 -1.2579750924899842 1.4258916086606965 1 1 3.7269849963023267 0 0 0
|
||||
5 1 0.6286896795685137 -1.0183343395119744 1.7689346339672825 1 1 3.7269849963023267 0 0 0
|
||||
6 2 0.7901522619067926 -0.6766341805565266 2.1540160705495754 1 1 3.7269849963023267 0 0 0
|
||||
7 3 0.7115777184886863 -0.40195579325143455 2.569568683291525 1 1 3.7269849963023267 0 0 0
|
||||
8 4 0.46973310377005234 -0.30251697967107033 3.0668007117519216 1 1 3.7269849963023267 0 0 0
|
||||
9 1 0.4056113349449848 -1.443775499211898 3.0590726503341124 2 1 3.7269849963023267 0 0 0
|
||||
10 2 -0.032028429059287516 -1.2947520971164723 2.7201071151392187 2 1 3.7269849963023267 0 0 0
|
||||
11 3 -0.31613855112314065 -0.908414175906161 2.4125207871782006 2 1 3.7269849963023267 0 0 0
|
||||
12 4 -0.38939391251821 -0.4866605488242819 2.006177777000426 2 1 3.7269849963023267 0 0 0
|
||||
13 1 -0.06232643040853296 -0.07155965522127403 1.5593206052730733 3 1 3.7269849963023267 0 0 0
|
||||
14 2 0.17884090390913376 -0.05516721349427172 1.021273149730912 3 1 3.7269849963023267 0 0 0
|
||||
15 3 0.4513439961906 -0.23795607383274572 0.5957328539615993 3 1 3.7269849963023267 0 0 0
|
||||
16 4 0.5077649359807965 -0.5565625134533538 0.1655875784458841 3 1 3.7269849963023267 0 0 0
|
||||
|
||||
Velocities
|
||||
|
||||
1 0.05386890022865587 0.02262922525602673 0.24882291144736746 0.1772010258006941 -0.29588531700001014 -0.2624137503614725
|
||||
2 -0.03995003075629463 0.26969511063701984 -0.18986454548195664 -0.030614539375968176 -0.11769518931480599 0.040074702426473215
|
||||
3 -0.20784535295201376 -0.13628722357673043 -0.06062477950201746 -0.03676034584820381 -0.06308707793373186 -0.14798601576087625
|
||||
4 -0.23969824181316998 -0.5624721730878831 0.032474422905036715 -0.16523645965016515 0.2860623077030974 0.33543519753105877
|
||||
5 -0.16114897356828353 -0.22889697470760145 -0.13553324962649563 0.07151030852881342 -0.09415592891043179 0.13422881539312292
|
||||
6 -0.04701706588477693 0.19216715585110036 0.14588242791297215 0.09218622989776322 -0.5640128930702024 0.09287105657777776
|
||||
7 0.05098438305112513 -0.038459555522009595 -0.14244196285749675 0.3479046835475834 0.4244922695910593 -0.13582882604358357
|
||||
8 0.37827971348411926 -0.04953992506010833 0.1626392045834847 0.0442887659636129 0.07868414126013584 -0.12713600444325032
|
||||
9 0.04912038408665491 0.041260647318716696 0.012223856334495234 0.03282916621721876 -0.00012670547095256 0.155978785417696
|
||||
10 0.1939216183073483 0.11075235485381942 -0.0405050516019971 -0.17008135001813812 -0.4563093565840761 -0.30318513627039506
|
||||
11 -0.351360733920646 -0.18822419067535692 0.36147938199051305 -0.3708221604627426 -0.49108381825941216 0.09435948331955418
|
||||
12 -0.1188642917357977 0.22355282456551884 0.009265586122144348 -0.28230100188858365 0.10276485660828892 0.10175233476780697
|
||||
13 -0.1446616296238799 -0.11552059909787235 0.1331477187595642 -0.25498721890374343 0.2754663721641154 0.05806416868630132
|
||||
14 0.051547120035862544 -0.36611026510775635 -0.06630782880801242 -0.11999847173316518 0.0684476892288605 0.2161595932308759
|
||||
15 -0.20214244962091388 0.23341226933559608 0.008133374252278069 -0.17013911124135248 0.01870292260510287 -0.2682954134361106
|
||||
16 -0.19202131162868008 -0.08105295741355378 -0.0469350810885074 0.017332107652647588 -0.32876588862807693 0.1085334141225924
|
||||
|
||||
Bonds
|
||||
|
||||
1 1 1 2
|
||||
2 1 2 3
|
||||
3 1 3 4
|
||||
4 1 4 5
|
||||
5 1 5 6
|
||||
6 1 6 7
|
||||
7 1 7 8
|
||||
8 1 9 10
|
||||
9 1 10 11
|
||||
10 1 11 12
|
||||
11 1 13 14
|
||||
12 1 14 15
|
||||
13 1 15 16
|
||||
|
||||
Ellipsoids
|
||||
|
||||
1 1.173984503142341 1.173984503142341 1.173984503142341 0.9964752158482045 -0.053253555733239796 0.011391163807102514 -0.06380787090289707
|
||||
2 1.173984503142341 1.173984503142341 1.173984503142341 0.9369923833143513 0.11220716044648564 0.06732538499716349 0.3239168400846305
|
||||
3 1.173984503142341 1.173984503142341 1.173984503142341 0.797964932091827 0.14473096354527873 0.18374142699366386 0.5554673737937029
|
||||
4 1.173984503142341 1.173984503142341 1.173984503142341 0.5660864821344559 0.14688275499481052 0.09873742533340191 0.8051226439917721
|
||||
5 1.173984503142341 1.173984503142341 1.173984503142341 0.2533023785125306 0.12062313161679827 0.08583012223905846 0.9559922359911086
|
||||
6 1.173984503142341 1.173984503142341 1.173984503142341 -0.03855807343534716 0.08405913137017908 0.02236505169306371 0.9954632800204194
|
||||
7 1.173984503142341 1.173984503142341 1.173984503142341 -0.45592844330248017 0.1004550065061007 -0.052524745294758785 0.8827679181910482
|
||||
8 1.173984503142341 1.173984503142341 1.173984503142341 0.768021221540491 -0.009582139884533599 0.03658677589040892 -0.63930665074644
|
||||
9 1.173984503142341 1.173984503142341 1.173984503142341 -0.23299975754512345 0.688686395231341 0.6747873944883376 -0.12682324016841584
|
||||
10 1.173984503142341 1.173984503142341 1.173984503142341 -0.24662061871907232 0.8744456399178389 0.39370836087823996 -0.13970261209395163
|
||||
11 1.173984503142341 1.173984503142341 1.173984503142341 -0.087475900850909 0.977367602388229 0.14493549113095577 -0.12686307572668784
|
||||
12 1.173984503142341 1.173984503142341 1.173984503142341 -0.03181169300779214 0.9634374984140112 -0.2442360692534371 -0.10547485630879185
|
||||
13 1.173984503142341 1.173984503142341 1.173984503142341 -0.032786070696572266 0.7922941528811777 -0.6084214170523915 -0.03191282109962717
|
||||
14 1.173984503142341 1.173984503142341 1.173984503142341 0.047188686288341455 0.6316396208287698 -0.7737349519945348 0.011783095844627799
|
||||
15 1.173984503142341 1.173984503142341 1.173984503142341 -0.05869980642620335 -0.34229358203414423 0.9376740835056508 0.012519965878508689
|
||||
16 1.173984503142341 1.173984503142341 1.173984503142341 -0.08582818143150042 0.0008707732197394232 0.9939540921464659 -0.0684691735853161
|
||||
@ -0,0 +1,73 @@
|
||||
variable number equal 2
|
||||
variable ofreq equal 1000
|
||||
variable efreq equal 1000
|
||||
variable T equal 0.1
|
||||
variable rhos equal 0.5
|
||||
|
||||
units lj
|
||||
|
||||
dimension 3
|
||||
|
||||
newton on
|
||||
|
||||
boundary p p p
|
||||
|
||||
atom_style hybrid bond ellipsoid oxdna
|
||||
atom_modify sort 0 1.0
|
||||
|
||||
# Pair interactions require lists of neighbours to be calculated
|
||||
neighbor 2.0 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
read_data data.duplex2
|
||||
|
||||
set atom * mass 3.1575
|
||||
|
||||
group all type 1 4
|
||||
|
||||
# oxRNA2 bond interactions - FENE backbone
|
||||
bond_style oxrna2/fene
|
||||
bond_coeff * oxrna2_lj.cgdna
|
||||
special_bonds lj 0 1 1
|
||||
|
||||
# oxRNA2 pair interactions
|
||||
pair_style hybrid/overlay oxrna2/excv oxrna2/stk oxrna2/hbond oxrna2/xstk oxrna2/coaxstk oxrna2/dh
|
||||
pair_coeff * * oxrna2/excv oxrna2_lj.cgdna
|
||||
pair_coeff * * oxrna2/stk seqdep 0.1 1.40206 2.77 oxrna2_lj.cgdna
|
||||
pair_coeff * * oxrna2/hbond seqdep oxrna2_lj.cgdna
|
||||
pair_coeff 1 4 oxrna2/hbond seqdep oxrna2_lj.cgdna
|
||||
pair_coeff 2 3 oxrna2/hbond seqdep oxrna2_lj.cgdna
|
||||
pair_coeff 3 4 oxrna2/hbond seqdep oxrna2_lj.cgdna
|
||||
pair_coeff * * oxrna2/xstk oxrna2_lj.cgdna
|
||||
pair_coeff * * oxrna2/coaxstk oxrna2_lj.cgdna
|
||||
pair_coeff * * oxrna2/dh 0.1 0.5 oxrna2_lj.cgdna
|
||||
|
||||
# NVE ensemble
|
||||
fix 1 all nve/asphere
|
||||
#fix 2 all langevin ${T} ${T} 2.5 457145 angmom 10
|
||||
|
||||
timestep 1e-5
|
||||
|
||||
#comm_style tiled
|
||||
fix 3 all balance 1000 1.03 shift xyz 10 1.03
|
||||
comm_modify cutoff 3.8
|
||||
|
||||
compute quat all property/atom quatw quati quatj quatk
|
||||
|
||||
compute erot all erotate/asphere
|
||||
compute ekin all ke
|
||||
compute epot all pe
|
||||
variable erot equal c_erot
|
||||
variable ekin equal c_ekin
|
||||
variable epot equal c_epot
|
||||
variable etot equal c_erot+c_ekin+c_epot
|
||||
fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
|
||||
|
||||
dump out all custom ${ofreq} out.${number}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz
|
||||
dump_modify out sort id
|
||||
dump_modify out format line "%d %d %d %22.15le %22.15le %22.15le %d %d %d %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le"
|
||||
|
||||
run 1000000
|
||||
|
||||
write_data last_config.${number}.* nocoeff
|
||||
#write_restart last_config.${number}.*
|
||||
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
@ -0,0 +1 @@
|
||||
../../../../../../../potentials/oxrna2_lj.cgdna
|
||||
@ -0,0 +1,68 @@
|
||||
LAMMPS data file in real units via oxdna lj2real.py, date 2024-05-19
|
||||
|
||||
10 atoms
|
||||
4 atom types
|
||||
8 bonds
|
||||
1 bond types
|
||||
10 ellipsoids
|
||||
|
||||
-170 170 xlo xhi
|
||||
-170 170 ylo yhi
|
||||
-170 170 zlo zhi
|
||||
|
||||
Masses
|
||||
|
||||
1 315.8376
|
||||
2 315.8376
|
||||
3 315.8376
|
||||
4 315.8376
|
||||
|
||||
Atoms # hybrid
|
||||
|
||||
1 1 -2.8740969069282687 -3.723118600434732 5.494693518792015 1 1 1.0016462505133576 0 0 0
|
||||
2 2 -2.7379071878387986 -6.079929519421481 10.066032484018534 1 1 1.0016462505133576 0 0 0
|
||||
3 3 -1.110437385073819 -7.791537941948432 13.848676172779387 1 1 1.0016462505133576 0 0 0
|
||||
4 4 1.4306089998272526 -8.354886654263622 17.79828313773629 1 1 1.0016462505133576 0 0 0
|
||||
5 1 3.9498326729322186 -6.646891787969407 20.657842369456382 1 1 1.0016462505133576 0 0 0
|
||||
6 4 -3.801540967989063 0.7719150486872158 21.01300417274477 2 1 1.0016462505133576 0 0 0
|
||||
7 1 -0.287657468030243 1.787063409177335 17.702181979507532 2 1 1.0016462505133576 0 0 0
|
||||
8 2 2.8086617684512323 1.5040732709582532 14.656350509768911 2 1 1.0016462505133576 0 0 0
|
||||
9 3 5.165059071666839 0.3988634556159852 10.50699529001116 2 1 1.0016462505133576 0 0 0
|
||||
10 4 6.817789789050184 -3.1038996716078557 8.419212766646357 2 1 1.0016462505133576 0 0 0
|
||||
|
||||
Velocities
|
||||
|
||||
1 0.0015993537866009029 -0.000680681865016988 -0.00014678467473993874 1.3034875452014287 -0.6725260292370423 1.5263182328899618
|
||||
2 0.0008422431968202534 -0.0002471920411024751 0.0007894382186365997 -0.32615096872390803 -0.0034351199136194157 -0.9136220137417161
|
||||
3 -0.0011446153381118452 0.00041850425643063176 -0.00045926941555484915 1.7184317758530245 2.6050996986101502 -0.47065934236730145
|
||||
4 -0.0011077496385743138 0.0002472924939324634 -0.00034633314311123244 -0.5778245520276679 1.752085001878762 -0.24048635097513535
|
||||
5 0.0004072478403200556 -0.0012804934445473403 0.0008610591638760516 0.23142339993018143 0.3972766524238825 1.363641236078021
|
||||
6 0.00017968178785700138 -0.00024308968845109275 0.00014280408309295725 0.1704955558294103 -1.3525913126172677 1.5501424653239764
|
||||
7 -4.108556803115003e-05 0.00023724044475488887 -0.00013843701960263193 0.7809156374181498 -2.1218743676572576 0.2975087875146955
|
||||
8 -0.00035835254321313353 0.0008579277312926632 0.0019500603503724006 -0.711656157643413 -2.0351916264105014 -0.7613827970610736
|
||||
9 -0.0008730894357027041 -0.00039026927657647716 0.0002796967510539106 -1.193834703375802 1.023301140813147 -1.8342354268493246
|
||||
10 0.0009421885758929626 -0.0005326396944231774 0.0006296458639527654 -0.24420734152643714 1.5633648178267814 0.6376075187926279
|
||||
|
||||
Bonds
|
||||
|
||||
1 1 1 2
|
||||
2 1 2 3
|
||||
3 1 3 4
|
||||
4 1 4 5
|
||||
5 1 6 7
|
||||
6 1 7 8
|
||||
7 1 8 9
|
||||
8 1 9 10
|
||||
|
||||
Ellipsoids
|
||||
|
||||
1 9.999999997766462 9.999999997766462 9.999999997766462 0.9890278201757743 0.01779228232037064 -0.14337734159225404 0.030827642240801516
|
||||
2 9.999999997766462 9.999999997766462 9.999999997766462 0.939687458852748 0.04174166924055095 -0.023337773785056866 0.338674565089608
|
||||
3 9.999999997766462 9.999999997766462 9.999999997766462 0.8210113150655425 0.03012140921736572 0.017666019956944813 0.5698429897612057
|
||||
4 9.999999997766462 9.999999997766462 9.999999997766462 0.6623662858285051 -0.028186343967346823 0.022942552517501488 0.7482981175276918
|
||||
5 9.999999997766462 9.999999997766462 9.999999997766462 0.3601488726765216 0.0513614985821682 0.0724224158335286 0.9286602067807472
|
||||
6 9.999999997766462 9.999999997766462 9.999999997766462 0.11941234710084649 0.9244660117493703 -0.35317942248051865 -0.07979711784524246
|
||||
7 9.999999997766462 9.999999997766462 9.999999997766462 -0.17949125421205164 0.7412884899431119 -0.6379094464220707 0.1065166771202199
|
||||
8 9.999999997766462 9.999999997766462 9.999999997766462 -0.10483691088405202 0.5508895999584645 -0.8250090480220789 0.06992811634525403
|
||||
9 9.999999997766462 9.999999997766462 9.999999997766462 0.07777239911646 -0.3724087549185288 0.9103052384821374 -0.1631181963720798
|
||||
10 9.999999997766462 9.999999997766462 9.999999997766462 0.16279109707978262 0.027148630125149613 0.9849325709665359 -0.0516705065113425
|
||||
@ -0,0 +1,71 @@
|
||||
# LAMMPS input file in real units via oxdna lj2real.py, date 2024-05-19
|
||||
variable number equal 1
|
||||
variable ofreq equal 1000
|
||||
variable efreq equal 1000
|
||||
variable T equal 300.0
|
||||
|
||||
units real
|
||||
|
||||
dimension 3
|
||||
|
||||
newton on
|
||||
|
||||
boundary p p p
|
||||
|
||||
atom_style hybrid bond ellipsoid oxdna
|
||||
atom_modify sort 0 8.518
|
||||
|
||||
# Pair interactions require lists of neighbours to be calculated
|
||||
neighbor 17.036 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
read_data data.duplex1
|
||||
|
||||
set atom * mass 315.8376
|
||||
|
||||
group all type 1 4
|
||||
|
||||
# oxDNA bond interactions - FENE backbone
|
||||
bond_style oxdna/fene
|
||||
bond_coeff * 11.92337812042065 2.1295 6.409795
|
||||
special_bonds lj 0 1 1
|
||||
|
||||
# oxDNA pair interactions
|
||||
pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk
|
||||
pair_coeff * * oxdna/excv 11.92337812042065 5.9626 5.74965 11.92337812042065 4.38677 4.259 11.92337812042065 2.81094 2.72576
|
||||
pair_coeff * * oxdna/stk seqav ${T} 8.01727944817084 0.005279604 0.70439070204273 3.4072 7.6662 2.72576 6.3885 1.3 0.0 0.8 0.9 0.0 0.95 0.9 0.0 0.95 2.0 0.65 2.0 0.65
|
||||
pair_coeff * * oxdna/hbond seqav 0.0 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0.0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45
|
||||
pair_coeff 1 4 oxdna/hbond seqav 6.42073911784652 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45
|
||||
pair_coeff 2 3 oxdna/hbond seqav 6.42073911784652 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45
|
||||
pair_coeff * * oxdna/xstk 3.9029021145006 4.89785 5.74965 4.21641 5.57929 2.25 0.791592654 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
|
||||
pair_coeff * * oxdna/coaxstk 3.77965257404268 3.4072 5.1108 1.87396 4.94044 2.0 2.541592654 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2 -0.65 2 -0.65
|
||||
|
||||
# NVE ensemble
|
||||
fix 1 all nve/asphere
|
||||
#fix 2 all langevin ${T} ${T} 4265.0 457145 angmom 10
|
||||
|
||||
timestep 0.01706
|
||||
|
||||
#comm_style tiled
|
||||
fix 3 all balance 1000 1.03 shift xyz 10 1.03
|
||||
comm_modify cutoff 32.4
|
||||
|
||||
compute quat all property/atom quatw quati quatj quatk
|
||||
|
||||
compute erot all erotate/asphere
|
||||
compute ekin all ke
|
||||
compute epot all pe
|
||||
variable erot equal c_erot
|
||||
variable ekin equal c_ekin
|
||||
variable epot equal c_epot
|
||||
variable etot equal c_erot+c_ekin+c_epot
|
||||
fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
|
||||
|
||||
dump out all custom ${ofreq} out.${number}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz
|
||||
dump_modify out sort id
|
||||
dump_modify out format line "%d %d %d %22.15le %22.15le %22.15le %d %d %d %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le"
|
||||
|
||||
run 1000000
|
||||
|
||||
write_data last_config.${number}.* nocoeff
|
||||
#write_restart last_config.${number}.*
|
||||
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
@ -0,0 +1,91 @@
|
||||
LAMMPS data file in real units via oxdna lj2real.py, date 2024-05-19
|
||||
|
||||
16 atoms
|
||||
4 atom types
|
||||
13 bonds
|
||||
1 bond types
|
||||
16 ellipsoids
|
||||
|
||||
-170 170 xlo xhi
|
||||
-170 170 ylo yhi
|
||||
-170 170 zlo zhi
|
||||
|
||||
Masses
|
||||
|
||||
1 315.8376
|
||||
2 315.8376
|
||||
3 315.8376
|
||||
4 315.8376
|
||||
|
||||
Atoms # hybrid
|
||||
|
||||
1 1 -5.224492277936935 -5.6003990662830665 3.072035980595378 1 1 1.0016462505133576 0 0 0
|
||||
2 2 -3.855482258589815 -8.54410812515585 6.182955020430966 1 1 1.0016462505133576 0 0 0
|
||||
3 3 -0.8418698080395857 -10.56041032511679 9.10967975032824 1 1 1.0016462505133576 0 0 0
|
||||
4 4 2.502394065492512 -10.715431837829685 12.145744722571814 1 1 1.0016462505133576 0 0 0
|
||||
5 1 5.355178690564601 -8.674171903962998 15.067785212133312 1 1 1.0016462505133576 0 0 0
|
||||
6 2 6.7305169669220595 -5.763569949980494 18.347908888941284 1 1 1.0016462505133576 0 0 0
|
||||
7 3 6.061219006086631 -3.4238594469157198 21.88758604427721 1 1 1.0016462505133576 0 0 0
|
||||
8 4 4.001186577913306 -2.576839632838177 26.12300846270287 1 1 1.0016462505133576 0 0 0
|
||||
9 1 3.454997351061381 -12.298079702286948 26.05718083554597 2 1 1.0016462505133576 0 0 0
|
||||
10 2 -0.2728181587270111 -11.028698363238112 23.169872406755868 2 1 1.0016462505133576 0 0 0
|
||||
11 3 -2.692868178466912 -7.73787195036868 20.549852065183913 2 1 1.0016462505133576 0 0 0
|
||||
12 4 -3.316857346830113 -4.145374554885233 17.08862230448963 2 1 1.0016462505133576 0 0 0
|
||||
13 1 -0.5308965342198838 -0.6095451431748122 13.28229291571604 3 1 1.0016462505133576 0 0 0
|
||||
14 2 1.5233668194980015 -0.46991432454420656 8.699204689407908 3 1 1.0016462505133576 0 0 0
|
||||
15 3 3.844548159551531 -2.026909836907328 5.074452450044903 3 1 1.0016462505133576 0 0 0
|
||||
16 4 4.325141724684425 -4.740799489595668 1.4104749932020408 3 1 1.0016462505133576 0 0 0
|
||||
|
||||
Velocities
|
||||
|
||||
1 0.00026896558742537556 0.00011298695236274073 0.001242364337461123 0.7538466533118467 -1.2587520584415195 -1.1163576881067447
|
||||
2 -0.00019946914535880285 0.0013465785184092233 -0.0009479872206420321 -0.13024003640483983 -0.5006975787807386 0.17048535791572514
|
||||
3 -0.0010377647810347322 -0.0006804774738725614 -0.000302697462953215 -0.15638545864527348 -0.2683843524758034 -0.6295604792026762
|
||||
4 -0.0011968051721949484 -0.002808404437492725 0.00016214368951061121 -0.7029471277015998 1.2169631204234201 1.42700472482703
|
||||
5 -0.0008046113463391788 -0.001142874812754601 -0.0006767129075723855 0.304218367349499 -0.4005571162913614 0.5710347488390389
|
||||
6 -0.00023475461149269044 0.000959484075931813 0.0007283860029089665 0.3921776444343422 -2.399417440979843 0.3950910265578085
|
||||
7 0.0002545632912247854 -0.00019202725318668095 -0.0007112078778547229 1.4800522749729792 1.8058703404340948 -0.5778414965351256
|
||||
8 0.0018887377488028885 -0.0002473511615838234 0.0008120520191337178 0.18841278062652408 0.3347372075847072 -0.5408605905745774
|
||||
9 0.0002452564077667799 0.00020601300929708606 6.1033299095680186e-05 0.13966147753401867 -0.0005390290197378453 0.6635632318913824
|
||||
10 0.000968244047328249 0.0005529827424647325 -0.00020224034557198784 -0.7235582069719148 -1.9412262416735993 -1.289806869224333
|
||||
11 -0.0017543321990246556 -0.000939796984860897 0.0018048542648271923 -1.5775475529872025 -2.0891633737315023 0.40142307521789933
|
||||
12 -0.0005934853675296159 0.001116191652783757 4.626275649966328e-05 -1.200961814632207 0.4371811217355096 0.43287366246768927
|
||||
13 -0.0007222905985558083 -0.0005767904238661645 0.0006648020330562531 -1.084763819731394 1.1718860080947717 0.2470159472481526
|
||||
14 0.0002573730178578412 -0.00182797610679242 -0.00033107273492769625 -0.510496177490122 0.29118940603730814 0.9195837620128926
|
||||
15 -0.0010092903785878923 0.0011654195253227475 4.0609661125969864e-05 -0.723803934131871 0.07956576746268508 -1.1413793944128399
|
||||
16 -0.0009587558806876301 -0.0004046946607553641 -0.0002343452641922075 0.07373406158203998 -1.3986322243084912 0.4617216556119086
|
||||
|
||||
Bonds
|
||||
|
||||
1 1 1 2
|
||||
2 1 2 3
|
||||
3 1 3 4
|
||||
4 1 4 5
|
||||
5 1 5 6
|
||||
6 1 6 7
|
||||
7 1 7 8
|
||||
8 1 9 10
|
||||
9 1 10 11
|
||||
10 1 11 12
|
||||
11 1 13 14
|
||||
12 1 14 15
|
||||
13 1 15 16
|
||||
|
||||
Ellipsoids
|
||||
|
||||
1 9.999999997766462 9.999999997766462 9.999999997766462 0.9964752158482045 -0.053253555733239796 0.011391163807102514 -0.06380787090289707
|
||||
2 9.999999997766462 9.999999997766462 9.999999997766462 0.9369923833143513 0.11220716044648564 0.06732538499716349 0.3239168400846305
|
||||
3 9.999999997766462 9.999999997766462 9.999999997766462 0.797964932091827 0.14473096354527873 0.18374142699366386 0.5554673737937029
|
||||
4 9.999999997766462 9.999999997766462 9.999999997766462 0.5660864821344559 0.14688275499481052 0.09873742533340191 0.8051226439917721
|
||||
5 9.999999997766462 9.999999997766462 9.999999997766462 0.2533023785125306 0.12062313161679827 0.08583012223905846 0.9559922359911086
|
||||
6 9.999999997766462 9.999999997766462 9.999999997766462 -0.03855807343534716 0.08405913137017908 0.02236505169306371 0.9954632800204194
|
||||
7 9.999999997766462 9.999999997766462 9.999999997766462 -0.45592844330248017 0.1004550065061007 -0.052524745294758785 0.8827679181910482
|
||||
8 9.999999997766462 9.999999997766462 9.999999997766462 0.768021221540491 -0.009582139884533599 0.03658677589040892 -0.63930665074644
|
||||
9 9.999999997766462 9.999999997766462 9.999999997766462 -0.23299975754512345 0.688686395231341 0.6747873944883376 -0.12682324016841584
|
||||
10 9.999999997766462 9.999999997766462 9.999999997766462 -0.24662061871907232 0.8744456399178389 0.39370836087823996 -0.13970261209395163
|
||||
11 9.999999997766462 9.999999997766462 9.999999997766462 -0.087475900850909 0.977367602388229 0.14493549113095577 -0.12686307572668784
|
||||
12 9.999999997766462 9.999999997766462 9.999999997766462 -0.03181169300779214 0.9634374984140112 -0.2442360692534371 -0.10547485630879185
|
||||
13 9.999999997766462 9.999999997766462 9.999999997766462 -0.032786070696572266 0.7922941528811777 -0.6084214170523915 -0.03191282109962717
|
||||
14 9.999999997766462 9.999999997766462 9.999999997766462 0.047188686288341455 0.6316396208287698 -0.7737349519945348 0.011783095844627799
|
||||
15 9.999999997766462 9.999999997766462 9.999999997766462 -0.05869980642620335 -0.34229358203414423 0.9376740835056508 0.012519965878508689
|
||||
16 9.999999997766462 9.999999997766462 9.999999997766462 -0.08582818143150042 0.0008707732197394232 0.9939540921464659 -0.0684691735853161
|
||||
@ -0,0 +1,71 @@
|
||||
# LAMMPS input file in real units via oxdna lj2real.py, date 2024-05-19
|
||||
variable number equal 2
|
||||
variable ofreq equal 1000
|
||||
variable efreq equal 1000
|
||||
variable T equal 300.0
|
||||
|
||||
units real
|
||||
|
||||
dimension 3
|
||||
|
||||
newton on
|
||||
|
||||
boundary p p p
|
||||
|
||||
atom_style hybrid bond ellipsoid oxdna
|
||||
atom_modify sort 0 8.518
|
||||
|
||||
# Pair interactions require lists of neighbours to be calculated
|
||||
neighbor 17.036 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
read_data data.duplex2
|
||||
|
||||
set atom * mass 315.8376
|
||||
|
||||
group all type 1 4
|
||||
|
||||
# oxDNA bond interactions - FENE backbone
|
||||
bond_style oxdna/fene
|
||||
bond_coeff * 11.92337812042065 2.1295 6.409795
|
||||
special_bonds lj 0 1 1
|
||||
|
||||
# oxDNA pair interactions
|
||||
pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk
|
||||
pair_coeff * * oxdna/excv 11.92337812042065 5.9626 5.74965 11.92337812042065 4.38677 4.259 11.92337812042065 2.81094 2.72576
|
||||
pair_coeff * * oxdna/stk seqav ${T} 8.01727944817084 0.005279604 0.70439070204273 3.4072 7.6662 2.72576 6.3885 1.3 0.0 0.8 0.9 0.0 0.95 0.9 0.0 0.95 2.0 0.65 2.0 0.65
|
||||
pair_coeff * * oxdna/hbond seqav 0.0 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0.0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45
|
||||
pair_coeff 1 4 oxdna/hbond seqav 6.42073911784652 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45
|
||||
pair_coeff 2 3 oxdna/hbond seqav 6.42073911784652 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45
|
||||
pair_coeff * * oxdna/xstk 3.9029021145006 4.89785 5.74965 4.21641 5.57929 2.25 0.791592654 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
|
||||
pair_coeff * * oxdna/coaxstk 3.77965257404268 3.4072 5.1108 1.87396 4.94044 2.0 2.541592654 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2 -0.65 2 -0.65
|
||||
|
||||
# NVE ensemble
|
||||
fix 1 all nve/asphere
|
||||
fix 2 all langevin ${T} ${T} 4265.0 457145 angmom 10
|
||||
|
||||
timestep 0.01706
|
||||
|
||||
#comm_style tiled
|
||||
fix 3 all balance 1000 1.03 shift xyz 10 1.03
|
||||
comm_modify cutoff 32.4
|
||||
|
||||
compute quat all property/atom quatw quati quatj quatk
|
||||
|
||||
compute erot all erotate/asphere
|
||||
compute ekin all ke
|
||||
compute epot all pe
|
||||
variable erot equal c_erot
|
||||
variable ekin equal c_ekin
|
||||
variable epot equal c_epot
|
||||
variable etot equal c_erot+c_ekin+c_epot
|
||||
fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
|
||||
|
||||
dump out all custom ${ofreq} out.${number}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz
|
||||
dump_modify out sort id
|
||||
dump_modify out format line "%d %d %d %22.15le %22.15le %22.15le %d %d %d %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le"
|
||||
|
||||
run 1000000
|
||||
|
||||
write_data last_config.${number}.* nocoeff
|
||||
#write_restart last_config.${number}.*
|
||||
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
@ -0,0 +1,68 @@
|
||||
LAMMPS data file in real units via oxdna lj2real.py, date 2024-05-19
|
||||
|
||||
10 atoms
|
||||
4 atom types
|
||||
8 bonds
|
||||
1 bond types
|
||||
10 ellipsoids
|
||||
|
||||
-170 170 xlo xhi
|
||||
-170 170 ylo yhi
|
||||
-170 170 zlo zhi
|
||||
|
||||
Masses
|
||||
|
||||
1 315.8376
|
||||
2 315.8376
|
||||
3 315.8376
|
||||
4 315.8376
|
||||
|
||||
Atoms # hybrid
|
||||
|
||||
1 1 -2.8740969069282687 -3.723118600434732 5.494693518792015 1 1 1.0016462505133576 0 0 0
|
||||
2 2 -2.7379071878387986 -6.079929519421481 10.066032484018534 1 1 1.0016462505133576 0 0 0
|
||||
3 3 -1.110437385073819 -7.791537941948432 13.848676172779387 1 1 1.0016462505133576 0 0 0
|
||||
4 4 1.4306089998272526 -8.354886654263622 17.79828313773629 1 1 1.0016462505133576 0 0 0
|
||||
5 1 3.9498326729322186 -6.646891787969407 20.657842369456382 1 1 1.0016462505133576 0 0 0
|
||||
6 4 -3.801540967989063 0.7719150486872158 21.01300417274477 2 1 1.0016462505133576 0 0 0
|
||||
7 1 -0.287657468030243 1.787063409177335 17.702181979507532 2 1 1.0016462505133576 0 0 0
|
||||
8 2 2.8086617684512323 1.5040732709582532 14.656350509768911 2 1 1.0016462505133576 0 0 0
|
||||
9 3 5.165059071666839 0.3988634556159852 10.50699529001116 2 1 1.0016462505133576 0 0 0
|
||||
10 4 6.817789789050184 -3.1038996716078557 8.419212766646357 2 1 1.0016462505133576 0 0 0
|
||||
|
||||
Velocities
|
||||
|
||||
1 0.0015993537866009029 -0.000680681865016988 -0.00014678467473993874 1.3034875452014287 -0.6725260292370423 1.5263182328899618
|
||||
2 0.0008422431968202534 -0.0002471920411024751 0.0007894382186365997 -0.32615096872390803 -0.0034351199136194157 -0.9136220137417161
|
||||
3 -0.0011446153381118452 0.00041850425643063176 -0.00045926941555484915 1.7184317758530245 2.6050996986101502 -0.47065934236730145
|
||||
4 -0.0011077496385743138 0.0002472924939324634 -0.00034633314311123244 -0.5778245520276679 1.752085001878762 -0.24048635097513535
|
||||
5 0.0004072478403200556 -0.0012804934445473403 0.0008610591638760516 0.23142339993018143 0.3972766524238825 1.363641236078021
|
||||
6 0.00017968178785700138 -0.00024308968845109275 0.00014280408309295725 0.1704955558294103 -1.3525913126172677 1.5501424653239764
|
||||
7 -4.108556803115003e-05 0.00023724044475488887 -0.00013843701960263193 0.7809156374181498 -2.1218743676572576 0.2975087875146955
|
||||
8 -0.00035835254321313353 0.0008579277312926632 0.0019500603503724006 -0.711656157643413 -2.0351916264105014 -0.7613827970610736
|
||||
9 -0.0008730894357027041 -0.00039026927657647716 0.0002796967510539106 -1.193834703375802 1.023301140813147 -1.8342354268493246
|
||||
10 0.0009421885758929626 -0.0005326396944231774 0.0006296458639527654 -0.24420734152643714 1.5633648178267814 0.6376075187926279
|
||||
|
||||
Bonds
|
||||
|
||||
1 1 1 2
|
||||
2 1 2 3
|
||||
3 1 3 4
|
||||
4 1 4 5
|
||||
5 1 6 7
|
||||
6 1 7 8
|
||||
7 1 8 9
|
||||
8 1 9 10
|
||||
|
||||
Ellipsoids
|
||||
|
||||
1 9.999999997766462 9.999999997766462 9.999999997766462 0.9890278201757743 0.01779228232037064 -0.14337734159225404 0.030827642240801516
|
||||
2 9.999999997766462 9.999999997766462 9.999999997766462 0.939687458852748 0.04174166924055095 -0.023337773785056866 0.338674565089608
|
||||
3 9.999999997766462 9.999999997766462 9.999999997766462 0.8210113150655425 0.03012140921736572 0.017666019956944813 0.5698429897612057
|
||||
4 9.999999997766462 9.999999997766462 9.999999997766462 0.6623662858285051 -0.028186343967346823 0.022942552517501488 0.7482981175276918
|
||||
5 9.999999997766462 9.999999997766462 9.999999997766462 0.3601488726765216 0.0513614985821682 0.0724224158335286 0.9286602067807472
|
||||
6 9.999999997766462 9.999999997766462 9.999999997766462 0.11941234710084649 0.9244660117493703 -0.35317942248051865 -0.07979711784524246
|
||||
7 9.999999997766462 9.999999997766462 9.999999997766462 -0.17949125421205164 0.7412884899431119 -0.6379094464220707 0.1065166771202199
|
||||
8 9.999999997766462 9.999999997766462 9.999999997766462 -0.10483691088405202 0.5508895999584645 -0.8250090480220789 0.06992811634525403
|
||||
9 9.999999997766462 9.999999997766462 9.999999997766462 0.07777239911646 -0.3724087549185288 0.9103052384821374 -0.1631181963720798
|
||||
10 9.999999997766462 9.999999997766462 9.999999997766462 0.16279109707978262 0.027148630125149613 0.9849325709665359 -0.0516705065113425
|
||||
@ -0,0 +1,71 @@
|
||||
# LAMMPS input file in real units via oxdna lj2real.py, date 2024-05-19
|
||||
variable number equal 1
|
||||
variable ofreq equal 1000
|
||||
variable efreq equal 1000
|
||||
variable T equal 300.0
|
||||
|
||||
units real
|
||||
|
||||
dimension 3
|
||||
|
||||
newton on
|
||||
|
||||
boundary p p p
|
||||
|
||||
atom_style hybrid bond ellipsoid oxdna
|
||||
atom_modify sort 0 8.518
|
||||
|
||||
# Pair interactions require lists of neighbours to be calculated
|
||||
neighbor 17.036 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
read_data data.duplex1
|
||||
|
||||
set atom * mass 315.8376
|
||||
|
||||
group all type 1 4
|
||||
|
||||
# oxDNA bond interactions - FENE backbone
|
||||
bond_style oxdna/fene
|
||||
bond_coeff * oxdna_real.cgdna
|
||||
special_bonds lj 0 1 1
|
||||
|
||||
# oxDNA pair interactions
|
||||
pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk
|
||||
pair_coeff * * oxdna/excv oxdna_real.cgdna
|
||||
pair_coeff * * oxdna/stk seqav ${T} 8.01727944817084 0.005279604 oxdna_real.cgdna
|
||||
pair_coeff * * oxdna/hbond seqav oxdna_real.cgdna
|
||||
pair_coeff 1 4 oxdna/hbond seqav oxdna_real.cgdna
|
||||
pair_coeff 2 3 oxdna/hbond seqav oxdna_real.cgdna
|
||||
pair_coeff * * oxdna/xstk oxdna_real.cgdna
|
||||
pair_coeff * * oxdna/coaxstk oxdna_real.cgdna
|
||||
|
||||
# NVE ensemble
|
||||
fix 1 all nve/asphere
|
||||
#fix 2 all langevin ${T} ${T} 4265.0 457145 angmom 10
|
||||
|
||||
timestep 0.01706
|
||||
|
||||
#comm_style tiled
|
||||
fix 3 all balance 1000 1.03 shift xyz 10 1.03
|
||||
comm_modify cutoff 32.4
|
||||
|
||||
compute quat all property/atom quatw quati quatj quatk
|
||||
|
||||
compute erot all erotate/asphere
|
||||
compute ekin all ke
|
||||
compute epot all pe
|
||||
variable erot equal c_erot
|
||||
variable ekin equal c_ekin
|
||||
variable epot equal c_epot
|
||||
variable etot equal c_erot+c_ekin+c_epot
|
||||
fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
|
||||
|
||||
dump out all custom ${ofreq} out.${number}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz
|
||||
dump_modify out sort id
|
||||
dump_modify out format line "%d %d %d %22.15le %22.15le %22.15le %d %d %d %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le"
|
||||
|
||||
run 1000000
|
||||
|
||||
write_data last_config.${number}.* nocoeff
|
||||
#write_restart last_config.${number}.*
|
||||
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
@ -0,0 +1 @@
|
||||
../../../../../../../potentials/oxdna_real.cgdna
|
||||
@ -0,0 +1,622 @@
|
||||
LAMMPS data file in real units via oxdna lj2real.py, date 2024-05-19
|
||||
|
||||
148 atoms
|
||||
4 atom types
|
||||
148 bonds
|
||||
1 bond types
|
||||
148 ellipsoids
|
||||
|
||||
0 851 xlo xhi
|
||||
0 851 ylo yhi
|
||||
0 851 zlo zhi
|
||||
|
||||
Masses
|
||||
|
||||
1 315.8376
|
||||
2 315.8376
|
||||
3 315.8376
|
||||
4 315.8376
|
||||
|
||||
Atoms # hybrid
|
||||
|
||||
1 1 208.31885120063512 209.07830059400624 213.0216021921939 1 1 1.0016462505133576 0 0 0
|
||||
2 4 208.94483576838627 206.4448010919165 216.6882923344523 1 1 1.0016462505133576 0 0 0
|
||||
3 3 211.56385346871699 204.30406864289688 220.11920728875927 1 1 1.0016462505133576 0 0 0
|
||||
4 2 214.31495335572012 204.35063728809808 223.61677544780568 1 1 1.0016462505133576 0 0 0
|
||||
5 1 217.30951997235965 206.16090626093134 225.4674912137906 1 1 1.0016462505133576 0 0 0
|
||||
6 2 219.30502197188136 209.00909667501074 227.49674701236893 1 1 1.0016462505133576 0 0 0
|
||||
7 3 219.83292281044646 212.19753274141107 230.53026977239148 1 1 1.0016462505133576 0 0 0
|
||||
8 2 218.93091557749156 214.31473141418766 234.6931272540053 1 1 1.0016462505133576 0 0 0
|
||||
9 4 220.32518751145957 214.85183803522298 239.6469648355356 1 1 1.0016462505133576 0 0 0
|
||||
10 2 219.79275827382872 213.3404053532149 243.70006386710043 1 1 1.0016462505133576 0 0 0
|
||||
11 3 220.70928151349608 210.21381004200654 247.14815553587854 1 1 1.0016462505133576 0 0 0
|
||||
12 2 223.67193733154724 208.04535577836813 249.67978988879284 1 1 1.0016462505133576 0 0 0
|
||||
13 2 227.31016552169513 206.16686658451448 251.61597827076264 1 1 1.0016462505133576 0 0 0
|
||||
14 1 231.80592101718645 204.9336536048614 251.53105173903185 1 1 1.0016462505133576 0 0 0
|
||||
15 2 236.2250804923752 205.47987477011685 250.98539881261863 1 1 1.0016462505133576 0 0 0
|
||||
16 3 240.0068773257833 207.77004331975903 249.53594241966383 1 1 1.0016462505133576 0 0 0
|
||||
17 1 242.98566065658693 210.5462682234126 249.63496548893542 1 1 1.0016462505133576 0 0 0
|
||||
18 4 245.42888445426894 214.27953740691964 250.53493716205472 1 1 1.0016462505133576 0 0 0
|
||||
19 2 248.78751685377597 216.90541434653767 253.53160552044426 1 1 1.0016462505133576 0 0 0
|
||||
20 4 251.39963359406735 218.16175894319667 257.62870661099066 1 1 1.0016462505133576 0 0 0
|
||||
21 2 255.5677235249031 217.61926364274564 260.07819570237643 1 1 1.0016462505133576 0 0 0
|
||||
22 3 259.63024332567574 215.18262726567113 260.69715353283686 1 1 1.0016462505133576 0 0 0
|
||||
23 1 263.1457867599882 212.6433935962059 258.9487935453862 1 1 1.0016462505133576 0 0 0
|
||||
24 1 266.3827446371434 210.87213953618837 256.26055100860737 1 1 1.0016462505133576 0 0 0
|
||||
25 2 267.97463902393866 210.20760693366043 251.4251108047254 1 1 1.0016462505133576 0 0 0
|
||||
26 3 270.07811694250654 210.90888555541903 247.7392596432837 1 1 1.0016462505133576 0 0 0
|
||||
27 1 271.09287437447114 213.11656552311496 244.5712139335691 1 1 1.0016462505133576 0 0 0
|
||||
28 4 272.8644901379567 216.09853596389848 242.34668607897146 1 1 1.0016462505133576 0 0 0
|
||||
29 3 277.14925724680575 218.15361661850437 241.02448320337692 1 1 1.0016462505133576 0 0 0
|
||||
30 2 281.6281862385014 219.54423347807102 240.83577460409623 1 1 1.0016462505133576 0 0 0
|
||||
31 4 285.53553117381364 218.07611082158127 239.4456849189117 1 1 1.0016462505133576 0 0 0
|
||||
32 2 288.8938226529956 215.3666526766779 237.57548982559325 1 1 1.0016462505133576 0 0 0
|
||||
33 1 291.12514756370877 212.98912935663924 233.8324040870632 1 1 1.0016462505133576 0 0 0
|
||||
34 4 291.3890795510732 210.45844522291486 230.3986316964525 1 1 1.0016462505133576 0 0 0
|
||||
35 2 290.3105820760069 208.74036664050792 226.7042745336879 1 1 1.0016462505133576 0 0 0
|
||||
36 4 289.18201447621146 208.91363527052587 222.89820557251684 1 1 1.0016462505133576 0 0 0
|
||||
37 2 288.971153902218 209.4805264669763 218.28666756836168 1 1 1.0016462505133576 0 0 0
|
||||
38 4 288.3534988328343 212.6173536934077 215.1661607036478 1 1 1.0016462505133576 0 0 0
|
||||
39 3 290.5684723991064 215.9608847032356 212.4583306861778 1 1 1.0016462505133576 0 0 0
|
||||
40 1 292.68130870382674 219.40449003374115 209.55910765683777 1 1 1.0016462505133576 0 0 0
|
||||
41 4 295.442338041982 219.36246849520484 206.48916887364152 1 1 1.0016462505133576 0 0 0
|
||||
42 2 296.36417522086 218.26244483114334 201.69379456148616 1 1 1.0016462505133576 0 0 0
|
||||
43 1 296.0323698080443 215.8225532800091 197.3280985778793 1 1 1.0016462505133576 0 0 0
|
||||
44 4 294.6530843322007 212.83142447716733 193.82965995050543 1 1 1.0016462505133576 0 0 0
|
||||
45 4 293.09410894134015 209.80599344824577 192.16605946359905 1 1 1.0016462505133576 0 0 0
|
||||
46 2 288.83490978178446 208.30134671602775 191.4877951864582 1 1 1.0016462505133576 0 0 0
|
||||
47 3 284.41597526830526 208.24835045301987 190.80522332231112 1 1 1.0016462505133576 0 0 0
|
||||
48 3 280.435589003895 210.25289346065463 190.2013738364397 1 1 1.0016462505133576 0 0 0
|
||||
49 1 276.458218418495 212.91127251248324 189.31964814095224 1 1 1.0016462505133576 0 0 0
|
||||
50 4 274.110573437327 215.08405186209467 186.3098121169227 1 1 1.0016462505133576 0 0 0
|
||||
51 2 272.2617942946457 216.3726311673256 182.27450679276578 1 1 1.0016462505133576 0 0 0
|
||||
52 2 269.83153994135154 216.05780869626503 177.8206876525648 1 1 1.0016462505133576 0 0 0
|
||||
53 3 267.4176400816519 213.93217536542784 174.3937134479138 1 1 1.0016462505133576 0 0 0
|
||||
54 2 263.3829580061682 212.17957495128988 172.47054426846077 1 1 1.0016462505133576 0 0 0
|
||||
55 2 259.23622219283226 208.62789572578382 172.79202606983338 1 1 1.0016462505133576 0 0 0
|
||||
56 1 254.9232399751811 207.98723446147798 174.1700423374239 1 1 1.0016462505133576 0 0 0
|
||||
57 1 251.01429470107985 207.4727826811597 176.6191860923174 1 1 1.0016462505133576 0 0 0
|
||||
58 4 247.503087519173 208.84937318781766 178.95270962305977 1 1 1.0016462505133576 0 0 0
|
||||
59 3 244.61228396290568 211.4487115261513 181.15392286257216 1 1 1.0016462505133576 0 0 0
|
||||
60 2 242.5582847227905 215.2537157253442 181.8226233142989 1 1 1.0016462505133576 0 0 0
|
||||
61 3 239.6649079158646 218.62799057023 180.73365427978584 1 1 1.0016462505133576 0 0 0
|
||||
62 2 235.1055006856569 219.4991097490642 179.19993338536528 1 1 1.0016462505133576 0 0 0
|
||||
63 2 230.06536838356837 218.20707751777684 178.12542542954407 1 1 1.0016462505133576 0 0 0
|
||||
64 1 226.19712505087438 216.01242228173862 178.66827050301285 1 1 1.0016462505133576 0 0 0
|
||||
65 4 223.80183977746594 212.48637324492603 181.4677574683601 1 1 1.0016462505133576 0 0 0
|
||||
66 2 223.35826983209282 209.42164303546804 184.31154729173656 1 1 1.0016462505133576 0 0 0
|
||||
67 4 223.115707961134 207.64116343000455 187.8227276328026 1 1 1.0016462505133576 0 0 0
|
||||
68 3 223.1828783897832 207.2041863918756 192.56176469772987 1 1 1.0016462505133576 0 0 0
|
||||
69 4 222.9562562898953 209.33623615586666 196.6941257026712 1 1 1.0016462505133576 0 0 0
|
||||
70 2 221.66690235711982 212.16853654386955 200.42093434949206 1 1 1.0016462505133576 0 0 0
|
||||
71 3 218.49749796817483 214.58613674743094 202.99887088045244 1 1 1.0016462505133576 0 0 0
|
||||
72 2 214.79843871210093 215.83998598169165 204.93838976343113 1 1 1.0016462505133576 0 0 0
|
||||
73 3 211.43258956470967 215.7076069451841 207.4075522992357 1 1 1.0016462505133576 0 0 0
|
||||
74 2 208.89304193837674 212.96791745700727 209.88970503949264 1 1 1.0016462505133576 0 0 0
|
||||
75 3 218.04384080398626 208.8517661220443 212.25851740130685 2 1 1.0016462505133576 0 0 0
|
||||
76 2 216.5892197279808 206.99598258539012 208.2068688237662 2 1 1.0016462505133576 0 0 0
|
||||
77 3 213.50296493867867 205.91838818342708 204.7824350973285 2 1 1.0016462505133576 0 0 0
|
||||
78 2 212.40344730057544 207.07794779056923 200.15488529641686 2 1 1.0016462505133576 0 0 0
|
||||
79 3 212.49899284410188 209.585331832834 196.59639195093382 2 1 1.0016462505133576 0 0 0
|
||||
80 1 213.8718296204717 212.43788517712443 194.07978733684686 2 1 1.0016462505133576 0 0 0
|
||||
81 2 217.77995345895644 215.8195741549278 192.62165385854775 2 1 1.0016462505133576 0 0 0
|
||||
82 1 221.28004012766087 217.1654248225849 190.47251220533374 2 1 1.0016462505133576 0 0 0
|
||||
83 3 225.8620451555664 217.7952321162026 189.70184485639834 2 1 1.0016462505133576 0 0 0
|
||||
84 1 229.11796505110405 216.62355134353226 188.55566261486354 2 1 1.0016462505133576 0 0 0
|
||||
85 4 231.93009597179287 213.28552897804775 187.18308633796394 2 1 1.0016462505133576 0 0 0
|
||||
86 3 233.8457023652249 210.92567784153482 183.76710295197495 2 1 1.0016462505133576 0 0 0
|
||||
87 3 235.10900957816648 209.21540627355986 179.91110079537762 2 1 1.0016462505133576 0 0 0
|
||||
88 2 237.54221305824186 209.88061882623805 175.87474946957948 2 1 1.0016462505133576 0 0 0
|
||||
89 3 240.73227695628347 211.91788237876028 172.5923540320211 2 1 1.0016462505133576 0 0 0
|
||||
90 2 244.20465175243865 215.00793672836622 171.518087640663 2 1 1.0016462505133576 0 0 0
|
||||
91 1 248.409983413366 216.8790144672266 172.84039701116973 2 1 1.0016462505133576 0 0 0
|
||||
92 4 252.3613185226405 217.80167017847748 174.7982475734568 2 1 1.0016462505133576 0 0 0
|
||||
93 4 255.03798994310935 216.90557703947596 178.41643036458865 2 1 1.0016462505133576 0 0 0
|
||||
94 3 258.0123600922758 214.0688621082654 181.3748252106654 2 1 1.0016462505133576 0 0 0
|
||||
95 3 261.4793208403472 211.18651636405338 182.10154093744066 2 1 1.0016462505133576 0 0 0
|
||||
96 2 264.61342330509945 208.4069633573196 182.13340389630036 2 1 1.0016462505133576 0 0 0
|
||||
97 3 268.1423255602099 206.43410772886958 180.6438100024248 2 1 1.0016462505133576 0 0 0
|
||||
98 3 272.6968293511453 206.12748243877718 180.10513377562995 2 1 1.0016462505133576 0 0 0
|
||||
99 1 277.10377489948667 208.1005328826892 179.3644456424518 2 1 1.0016462505133576 0 0 0
|
||||
100 4 281.00559845205873 211.06408209877605 180.10786289756504 2 1 1.0016462505133576 0 0 0
|
||||
101 2 284.60417782769156 214.3962696861514 181.99641804441617 2 1 1.0016462505133576 0 0 0
|
||||
102 2 286.60418124482914 216.5009851375199 185.7625155225522 2 1 1.0016462505133576 0 0 0
|
||||
103 3 287.3342876501778 217.90577178570192 189.82320249461165 2 1 1.0016462505133576 0 0 0
|
||||
104 1 287.1580072830518 218.24647026624564 194.54524399609593 2 1 1.0016462505133576 0 0 0
|
||||
105 1 285.97555699942546 216.4030183962319 198.00226153513316 2 1 1.0016462505133576 0 0 0
|
||||
106 4 286.9784674182509 213.80941634861662 200.984054131366 2 1 1.0016462505133576 0 0 0
|
||||
107 3 289.7070250162039 211.13118523574875 203.5459670820893 2 1 1.0016462505133576 0 0 0
|
||||
108 1 293.7348288391273 209.76614933968972 205.9159671580589 2 1 1.0016462505133576 0 0 0
|
||||
109 4 298.0470912443835 210.3476646132807 209.22602515661964 2 1 1.0016462505133576 0 0 0
|
||||
110 2 299.3727498239561 211.18882961507936 213.32359581947546 2 1 1.0016462505133576 0 0 0
|
||||
111 1 298.71438019179976 213.36502754336712 217.80809292107566 2 1 1.0016462505133576 0 0 0
|
||||
112 3 297.5778290486891 215.80813084505792 221.52375033983938 2 1 1.0016462505133576 0 0 0
|
||||
113 1 293.84181972000164 218.12459328726527 222.52194563573968 2 1 1.0016462505133576 0 0 0
|
||||
114 3 289.72480591547844 219.18763960036753 224.20582823532217 2 1 1.0016462505133576 0 0 0
|
||||
115 1 286.10060227835305 218.2366927723458 227.3329804786708 2 1 1.0016462505133576 0 0 0
|
||||
116 4 282.4274439426548 215.8348128129646 228.50667608915776 2 1 1.0016462505133576 0 0 0
|
||||
117 3 280.30736615533436 212.87615928361103 231.93191134907437 2 1 1.0016462505133576 0 0 0
|
||||
118 1 280.4957715892933 209.81978142604717 235.78978894134258 2 1 1.0016462505133576 0 0 0
|
||||
119 3 281.1124372652675 209.1630066603096 240.4037199441234 2 1 1.0016462505133576 0 0 0
|
||||
120 2 280.6004552189253 209.5904328052497 245.12986147761828 2 1 1.0016462505133576 0 0 0
|
||||
121 1 279.7088300157109 212.49871921998974 249.6398422165285 2 1 1.0016462505133576 0 0 0
|
||||
122 4 277.5145094311825 215.74407956221037 251.87908394986235 2 1 1.0016462505133576 0 0 0
|
||||
123 2 274.0292663881701 218.98094440600102 252.4720990110135 2 1 1.0016462505133576 0 0 0
|
||||
124 3 269.4802808363886 220.3779076053549 252.2846885821039 2 1 1.0016462505133576 0 0 0
|
||||
125 4 265.18702541695495 219.66875534535617 251.05221442068142 2 1 1.0016462505133576 0 0 0
|
||||
126 4 261.1973441761709 217.60856802642994 250.32297289687062 2 1 1.0016462505133576 0 0 0
|
||||
127 2 258.42965815651195 214.5285058619342 250.70264078825883 2 1 1.0016462505133576 0 0 0
|
||||
128 3 257.40131364348747 210.82918968859514 252.82205800210747 2 1 1.0016462505133576 0 0 0
|
||||
129 1 254.09665907944853 208.48587191866105 255.29832851571967 2 1 1.0016462505133576 0 0 0
|
||||
130 3 249.14711800822565 207.4790641809653 257.14454107837594 2 1 1.0016462505133576 0 0 0
|
||||
131 1 245.16232229032394 208.6542795519212 259.30366719951866 2 1 1.0016462505133576 0 0 0
|
||||
132 4 241.6088192401875 210.27052783917878 259.77711048596495 2 1 1.0016462505133576 0 0 0
|
||||
133 2 237.60579348133834 211.5677601936723 258.4967443170624 2 1 1.0016462505133576 0 0 0
|
||||
134 3 234.31563856213194 213.7023345421011 256.67498877187217 2 1 1.0016462505133576 0 0 0
|
||||
135 4 232.04178676973854 215.2247580978991 252.4887135012261 2 1 1.0016462505133576 0 0 0
|
||||
136 3 231.84989854624848 214.78206092351417 248.38409354076154 2 1 1.0016462505133576 0 0 0
|
||||
137 3 230.23584615132918 213.90825105541285 244.25659773796446 2 1 1.0016462505133576 0 0 0
|
||||
138 2 228.72514438427442 210.55975546279873 240.93389432997455 2 1 1.0016462505133576 0 0 0
|
||||
139 3 226.50901828126607 207.7720868061071 238.77244759668554 2 1 1.0016462505133576 0 0 0
|
||||
140 1 222.69524184571324 205.4563710695796 237.54896302353555 2 1 1.0016462505133576 0 0 0
|
||||
141 3 217.75254577305915 204.6697036863105 236.7300149978949 2 1 1.0016462505133576 0 0 0
|
||||
142 2 213.36264669166687 205.6664161637754 235.057769544392 2 1 1.0016462505133576 0 0 0
|
||||
143 3 210.36056196219099 208.22961038909222 233.43624218141468 2 1 1.0016462505133576 0 0 0
|
||||
144 4 209.52101940489996 211.7474752490511 229.6093465145509 2 1 1.0016462505133576 0 0 0
|
||||
145 3 210.0346178174762 213.46103317355895 225.4432866022292 2 1 1.0016462505133576 0 0 0
|
||||
146 2 212.1036301773736 214.37817428934144 222.09240510601887 2 1 1.0016462505133576 0 0 0
|
||||
147 1 214.8007196331168 213.86842062768343 219.12311053490302 2 1 1.0016462505133576 0 0 0
|
||||
148 4 217.11029191388695 212.18186978209044 215.47812529247457 2 1 1.0016462505133576 0 0 0
|
||||
|
||||
Velocities
|
||||
|
||||
1 0.00041441960428137935 -0.00044093526915074335 -0.0002769004051949902 0.4671811380872407 -0.45316000711452054 0.030147401411566938
|
||||
2 -0.0007883200593843776 0.0002582267767411247 -0.00015788826223433837 -0.9981841013239229 0.9031525891258723 -0.4463027445462194
|
||||
3 -0.00032890342226527046 0.00021454292082771174 0.0006588673608947611 1.6856487176959336 0.15828183663773915 -0.2816792383591273
|
||||
4 0.0006226412184223278 -0.0004819430644898339 0.0011543818273686507 0.771113570326925 0.9667209836529702 0.5390145490152992
|
||||
5 0.0008444214308690865 0.0006267645341900317 0.0009246638392575237 -0.9987251151971048 0.3864646803189593 -0.7699530964442148
|
||||
6 0.0009763171425943993 -0.0003909887231919038 -0.0009121871394260499 0.7366273192130102 -1.0054394417185868 0.7471606181669701
|
||||
7 -0.0003964811445218345 -0.0004173285602521412 -0.0007056214158470973 0.06052108734325723 -0.29784593755108146 0.7316972423378784
|
||||
8 3.7047285926338676e-05 -0.0002720689524084308 -0.00034613908102107556 0.20653978207022358 -0.5600630808371041 -0.7544747714740252
|
||||
9 -0.0007009303824597543 0.001556981461008396 0.0012173625702768208 -0.3788471824273982 0.42127744223658237 0.706230160987193
|
||||
10 -0.0015981160984836474 0.0004624234429405509 0.000633042527195227 0.9137264942274623 -0.0097229359145721 -1.5620769285620402
|
||||
11 -0.0006131679864152933 -0.0002837317754898309 -0.000596160114576507 -0.16060842579146267 -1.4682292580341976 1.662901421705255
|
||||
12 0.0014114099463271759 0.0013414818109726508 -0.0003789171466630028 0.2592330791173297 0.829986229089849 0.9413867863151553
|
||||
13 0.0007570391002086509 0.0008025872372338182 -7.972953403202178e-05 -0.17099323265046504 0.003517188802442484 0.5961537792303933
|
||||
14 -0.00046259381441702234 -0.00090135523551774 -0.00025506367753356103 -0.8790499857371116 0.6176988758143042 0.05832877360454661
|
||||
15 0.0017736622371445178 -0.00021639401439837712 0.0010865438562664787 -0.13139209450799721 0.8624674720612805 -0.011036817907692937
|
||||
16 9.079351638896072e-05 0.0006800971201785199 -0.00046628761539115553 0.7977461182616878 0.8586300458614435 0.5367785839788761
|
||||
17 0.0003320853011294431 4.9782060934935786e-05 -0.0010221421644623877 -0.6443212440432361 -0.11357760375273049 0.850108891065061
|
||||
18 -0.001273799512678254 0.0011802538929646376 0.00034715679420532845 1.148914164227578 -0.5610176349462389 0.5244301492446057
|
||||
19 -0.0020462501335023037 -0.0008081103285391302 0.0004315854879938803 -1.089683852796499 -0.32463478354041436 -0.7265732502745839
|
||||
20 -8.915796710513424e-05 0.00038580427801161824 -0.00046526527667176273 0.9097166769703294 0.5738252017630338 -1.29062344651377
|
||||
21 0.001415496055715896 0.0004065686658735653 -0.00010989062666979347 -1.1571187373784757 0.023561693505977636 -0.2263304187071502
|
||||
22 -0.0008503530592149795 2.8074460028882493e-05 0.00198633110988951 -0.4436460810940315 0.7384999777235214 1.558875871313546
|
||||
23 0.001213257612781923 0.0006312085806837118 0.00029437342449475603 0.6298784491419476 2.0523178203868553 -0.6191528692800492
|
||||
24 -0.0002744446284938336 -0.0011191784233664152 -0.000707033966844946 -0.09130366470337603 0.6760929751938499 1.0349559780864541
|
||||
25 0.0009651532852808743 -0.0011155857115756785 0.0007545732220657096 -1.2532487137150916 0.3253456368605829 -0.5895446662565031
|
||||
26 0.0013519355559207951 -0.0003602465335484942 4.0583375777164296e-05 0.3822696974424084 0.08729032133339974 0.41452369513711473
|
||||
27 -0.001665301320612367 -0.0007705885202069591 0.0005018578609282953 1.1334536456402204 1.9176030539077622 0.10183970014017323
|
||||
28 0.001737706168775158 8.21782568605148e-06 -0.0008049720960126812 -0.7476612511274086 2.2303524147696283 -1.0960603548956669
|
||||
29 0.001183967869191855 0.0007794707767112501 0.0011572550877270184 -0.8726708311148604 1.0159045767027794 -0.418256497806968
|
||||
30 0.00022506137173594954 0.0007997074716567607 -0.0007511442272268112 0.8112527327298255 -0.05903807219870134 0.623173366659473
|
||||
31 -0.0008847110697388197 -0.0003554831779230716 -0.0009329868015323094 0.5545451516333009 -0.29871375676152245 0.0890228395420963
|
||||
32 -0.0011265435872626274 0.00039619848780672557 -0.0012459482196480228 1.4457577029507602 -0.06889896003288522 -0.22324642105659825
|
||||
33 0.00023845768588633132 0.00044987471851870743 9.299879812422249e-06 0.7170427987947958 0.4983890283165274 0.4217807571946686
|
||||
34 8.32516030278601e-05 0.00021623128235669596 0.00028842186460696786 -0.7259246562112577 0.5751658269069845 -0.3694177872395038
|
||||
35 -0.00041861134337793226 -0.00020890877766567396 -0.0003835693263263161 -0.04356698055332095 0.4829754783161558 -0.7868946492403924
|
||||
36 -0.0021310793657824626 0.0005296179189949723 -1.836376297756258e-05 -1.6518357943020405 1.1542189579552737 -0.8600083978480586
|
||||
37 0.00034819323635394933 0.0005277328535131145 -0.0007890234683185679 0.06901830182094872 -1.0710751951395068 -0.9003668790915229
|
||||
38 -0.0004306890871425647 0.0007084036672237173 5.4006247807143286e-05 -0.29670175877751875 0.9535854791259951 1.3068905353981062
|
||||
39 -0.00032734838061953083 5.4267842460482285e-06 0.00035178461613378674 0.4482978794046991 0.2585368302398761 -1.4948626345393037
|
||||
40 0.000425960963436888 0.0004866264349846475 -0.00032754331069256257 1.354357422327269 -1.7371693097824732 -0.5387472817872587
|
||||
41 -0.00031121156230807574 -0.000557408138619122 0.0004581712062516314 -0.2462511006049055 0.754914814110346 1.5214208316099158
|
||||
42 0.0006138294415283338 -0.001475734146105284 0.0006932832392585454 -0.4279126916663162 0.31475284637140866 0.4947719379913577
|
||||
43 -0.00032901346057991044 0.002088241897437943 4.007591827893774e-06 0.8310167656169738 -2.0323789115861537 1.0346001003326915
|
||||
44 -0.00037100941050768806 -0.0006450300422373223 -0.000991826582086897 1.677913872230059 1.0355469382794293 -1.3207502139903968
|
||||
45 -0.0014015731274973644 -0.0012218924243723739 -0.00038363514183312886 0.21441712996148996 1.0043730062590748 -0.21165269663622438
|
||||
46 -0.0004431983077692244 0.0002428406842882312 -0.0006968537750801398 0.019488989787254087 0.5074153748008283 0.32784234392500033
|
||||
47 0.0002539699490763818 0.00013063672010696437 -0.0005621326124479586 1.1289132857339166 -0.4336732389495026 -1.4418229599456827
|
||||
48 0.0004898689039600226 0.0007527815950569443 0.00017691726070110023 -0.04005858674195536 -0.3740447543467191 -1.5655401179647614
|
||||
49 0.0001564078262564333 0.0013899183819377587 0.002136610172630379 -0.889719403762743 -0.2599617169154644 0.1451237505291117
|
||||
50 0.0010371837267272566 -0.00035833149145438357 -0.0003714320448076416 0.29638519543410047 -0.3977494984303205 -0.6105638314847442
|
||||
51 0.0009820602635995975 0.0007300099198006708 0.0001445457759367302 -0.7729541689963864 0.23499445513191905 -0.4948714964687896
|
||||
52 -0.0005457475822861008 -0.0006139596879639669 0.0001276859480116569 -1.2819675747397143 -0.9022146501313074 0.5188110087927617
|
||||
53 -0.0013460292907985106 -0.0006045929031479083 0.0009730685711565265 -0.5604204014611567 0.6294902790250949 0.30894138636009333
|
||||
54 0.0016274959548552353 -0.00034228237517440935 -0.00033120130942141594 0.8479051878078213 1.2771867984242118 0.52164182542914
|
||||
55 -0.0004834266647931496 -0.00020468767210863722 0.0005357651280403127 0.5748160751561723 0.8323411456475563 0.3520914227622347
|
||||
56 0.0004006310009063323 0.0004333955160002978 -0.00029974077755727616 0.21614599123688852 -0.20213469273624976 1.228193321040514
|
||||
57 0.00018436095379532414 0.0015151679397907168 -0.0008392194652949486 -1.3778465339123198 -0.08543711080164341 -1.3168477137462207
|
||||
58 -0.00026831588288024627 0.0004916472396323976 -0.0003466761300936674 -1.927389116565991 0.9121987357722435 0.6675708203587036
|
||||
59 -0.0006258690548135083 0.001297622079709614 -0.0008844486928368857 0.3311157072888594 0.7983313017995447 1.1270556542532257
|
||||
60 -0.00018043015007094488 1.568633521465739e-05 2.4469889031939575e-06 0.6098608205841689 0.06719653600738755 -0.6226068737246789
|
||||
61 0.0006670186871407943 0.0009368758878619058 -0.0006536612657749543 -0.08245254775216962 -0.13267665294317502 0.07402067490225707
|
||||
62 0.00024971794567419547 -0.00022528002682063684 0.0010317709111284002 -0.9577657247991458 -0.465567893792205 0.5392831535575356
|
||||
63 -0.00039872166876622647 0.001114681131409033 -0.00046664584809481623 0.5614397921385779 -0.03676601977717225 0.9239434081307943
|
||||
64 -0.00022428609950955975 -0.0012092952670300532 0.0003990757469131255 -1.3388937939722194 0.4998474396687487 1.007959495302009
|
||||
65 -0.0004760321453345616 -0.001118005263589924 -0.0018913930687617015 -0.004769150595413406 0.18816230253856664 0.8465936030278335
|
||||
66 -0.000569604752461696 0.0013664722826310341 0.0011885134090689172 -1.2862730133083389 -1.725300067226994 0.2460409197199418
|
||||
67 -0.0008303642114678211 -4.6765476279521475e-05 0.00013538897487258477 0.45014165664147954 -1.5560912795384267 0.49435961844291937
|
||||
68 -0.0004166480989256062 0.0007419400328216953 0.001640065264820625 0.8519022828028688 0.7773786853644404 0.10107332851893677
|
||||
69 0.000715049387221894 -0.0007845722675302896 0.00011171267588401845 1.4124312729529342 0.6732975396570777 -1.314868900890707
|
||||
70 0.0002899597770195227 0.000960176245563633 -1.2369804764834543e-05 -0.32958544017179037 -2.194591749536253 -0.013996371604443652
|
||||
71 -0.000784599438062652 -0.0007745814721290174 -0.0015598831332579418 -0.3116052477363819 0.16420020898354412 -1.6475074357573227
|
||||
72 -0.0012109413821898103 -0.0010259792078996565 0.002009002297714139 0.9464894936396385 -0.38422490798865216 -0.11388633123866836
|
||||
73 -0.0005770654505789276 0.0013960028145465113 -0.0009586405157593675 -2.2010719253995727 -0.5064523326977327 1.5912594523789898
|
||||
74 0.00045897496166799693 -0.0003571250431536989 0.00013956166316199796 0.36653957339486676 0.7750720539917312 2.2825538122361007
|
||||
75 -0.0007635787543225344 0.0009151095119275483 0.0003621989039139825 0.7533600338402616 -0.03709654588161272 -1.5048387303147006
|
||||
76 -0.0017782702176303371 -0.0001422139697962813 3.268639826972334e-05 1.0766718044834034 0.22754200372682035 1.4094207128249334
|
||||
77 -0.0009944633549961689 -2.7185643785831554e-05 0.00035935779588646224 -0.6249513355327749 0.026376668634114326 -0.5196033249835427
|
||||
78 0.0014525047108631406 -0.0002635250122154471 0.0002946308782002014 -1.0671559183404153 -0.1420073799791104 -0.8090786443688043
|
||||
79 -0.0001738312018541894 -0.0007956971705519024 0.0007051012709860657 0.9916562444273318 0.475176667924977 0.5186997764671554
|
||||
80 0.00020560278909850191 -0.00023794602258757743 9.508202338166986e-05 -0.2755538757376673 -0.08313141332877286 0.1736802978231154
|
||||
81 0.0007960466599558679 0.00019636226289575923 -0.00026344322077701926 0.1099307676035118 0.2970133171513775 -0.39383055555986834
|
||||
82 -0.0006439151111143676 0.0007368202530057124 -0.00020757692084898483 0.46488765978295077 -0.9104435244182589 -0.7977412027945551
|
||||
83 -0.0016373958881352256 -0.0008034248902800111 -0.0006475209926272188 -1.0629433685117573 0.32694393784433146 -0.38144155381771266
|
||||
84 -9.349877721927945e-05 -0.0012837405933129888 -0.0006913804447077405 0.005372083699246987 -0.5390925149085727 -0.2777575459740771
|
||||
85 7.175984873377987e-05 -8.188145840067058e-05 0.0002476795327649455 -0.4292240517999446 0.8471718983985552 -1.379191667891945
|
||||
86 -0.0019361003225944666 0.0008281345158297657 0.0012385275618332736 0.40376229600085867 -0.2593622200277787 -0.17852822534847618
|
||||
87 0.0013350477089695762 0.0016805760989646486 -0.00011902052738513388 0.6351408631430563 0.8905103709996127 0.6769065521869173
|
||||
88 -0.0006559832276122308 0.001068966018238896 6.191198328022662e-05 0.7743332510873531 -0.5636639470178074 0.881565119273955
|
||||
89 -0.000730455146994518 -0.0019469540223469542 0.00034279428798091206 -0.6705207281868615 0.6731271636970831 0.11003603539529515
|
||||
90 0.0005181357116835608 -6.261673348842832e-05 -0.0012048597515897858 -1.616761818914026 -0.13934277940905304 0.39022517259497297
|
||||
91 0.0006963262662605267 -7.783665730819486e-05 0.00011631757641122484 -0.3235934304904304 0.2505540998731511 -0.12891213834749454
|
||||
92 0.0011733692549690815 0.0012573921682906917 -0.001115727606719598 2.0498551640221705 -0.21195045002905308 1.5462260089037279
|
||||
93 0.0003012217343432592 0.001554968567194936 -0.00019150686295984871 -1.3764375241458235 -0.7169856499022497 -0.37962935868578923
|
||||
94 -0.001071413456691653 -0.0004530890205228453 0.000676953628648073 0.04300759511723225 0.4315824556425482 -1.6513162225610292
|
||||
95 -3.462073031939998e-05 -0.0007341336126085571 0.0007750028474385615 -0.01831437912190255 0.6452234717715252 0.5634104621702328
|
||||
96 0.00016908537517974456 0.0006881867158179877 -9.660314652542665e-05 0.750539978335223 0.3644557523491205 -1.149167318038805
|
||||
97 -0.0010727177207611647 -0.0002805275665690652 0.0009397207677218869 -0.6339140219416552 1.0638581171311459 0.4915823701624352
|
||||
98 9.141003584129238e-05 -0.0001182773394138833 -0.00017713640126118887 1.4896363726120205 0.725712306523633 -0.6955334599959595
|
||||
99 -0.0005329796862308534 -0.0002213644188271466 -0.0006880914995187214 1.3214262974710724 -0.5269665401199022 -0.5922300334343619
|
||||
100 -0.0002782784640981771 0.0004974233985925297 -0.001010298225495541 -0.9078341914823335 -0.535657056472583 0.26649700017402456
|
||||
101 0.000707029389827628 -0.0009053753028934495 -0.0005667802283044673 -0.6903835242905281 0.08929827857526158 0.89536066198302
|
||||
102 -0.0005252229792661067 0.0016195606485275703 -0.0006118175800384144 0.590342438029956 0.9957317636289214 2.2899526993955805
|
||||
103 0.0005513903544292183 -0.0006753190874512704 0.0008720377845095684 -1.8485190567648884 -0.5444534851188696 -0.049430494185178954
|
||||
104 -0.0005963338052002674 0.0018664586177513723 -6.124459534834667e-05 -1.7400426438973087 -0.8933939097574652 1.3270715145663594
|
||||
105 0.00018944831231515656 -0.0004257936154314862 -0.0002325330225103875 -0.20831100370485076 -0.31951119697135577 0.17363427769999923
|
||||
106 -0.0011657683659422825 0.00021341203878020944 -0.0016036743084162136 -0.8547196577896573 -0.2022779049615188 -0.2585575583483525
|
||||
107 -0.00014071663978679116 4.368679354729772e-05 0.0005913271451610716 0.26393148141343503 0.5118496584862787 -0.19630947726526438
|
||||
108 0.0008526353343687424 -0.0007047116463317371 -0.0003338667680450761 -0.8678172295210281 0.4772470148640593 -1.1972264029793078
|
||||
109 -0.00010998013637344678 -0.0012808467322045288 -0.00019333442850743478 0.35516627827753844 0.4812786306277344 -0.5845962387823183
|
||||
110 0.0013189714183481668 -0.0003625633061155731 0.00041103542234669806 0.7863916775761682 0.5066269134009194 0.22665104319035512
|
||||
111 -0.00013336910129714763 0.00015696055100528249 0.00029023065307822766 0.34873734012781815 1.5661898034091826 0.3776293771733237
|
||||
112 0.002163162431439717 0.00010327477645835898 0.00036287818767705284 -0.14951073355663014 -0.07190162661891987 -1.289133432993426
|
||||
113 -0.000686179472822298 -0.0005734723083885262 0.000596645854960574 -0.40297446498764145 -0.868123584934036 0.6091868845217895
|
||||
114 -0.00044255825584144006 9.173141744053142e-05 0.0010119556193854276 -0.8523759721019909 -0.21029695275901308 0.7202085310387388
|
||||
115 -0.0024321958386118937 0.00012828266889842094 -0.00012253996872963992 -0.06461511751249392 -0.6845316306479935 0.369115498378376
|
||||
116 -0.0007522288798272324 -0.001134542992781188 -0.0014242747759699364 -0.785220133384427 -0.6844982300111426 1.3214875798125256
|
||||
117 -0.001631336215163934 -0.0005620783715462203 0.000526273539346324 -0.6457028977302333 1.041323338492826 -1.5550332780972522
|
||||
118 0.0006791212566566071 0.0010831088146151281 -0.00031665664113898745 0.14270976262848908 0.1863524646960678 -0.6863985478211646
|
||||
119 -0.0005598304914650194 -0.0005445967376659685 0.00018420379420410263 0.18595611493782868 0.4422247424120456 -0.17695297797747686
|
||||
120 0.0013043539626961254 0.00018519112197755528 -0.0012774569712626503 -0.6115604054405038 0.0895062618517034 -0.3309825750831735
|
||||
121 -0.0009181250548043257 -4.111216227363675e-05 0.0008431381117500141 0.3336913187282888 -0.02587997063901842 -0.4563071067258067
|
||||
122 7.770442848786119e-05 -8.104535350298567e-05 -0.0021257280290162047 -1.1480690276494463 0.1553316041533672 -0.7074712585692718
|
||||
123 0.0011888332740761425 -0.000596477576403464 2.667537957250084e-05 -1.1276615053846293 -0.021528408791956666 -0.1224979914050052
|
||||
124 0.0016536945498203726 0.0013076448975284146 -0.0005474343104989092 0.6571092201608782 -0.992841406684317 0.4358321480511963
|
||||
125 -0.0010288694146039121 -0.0012382625011454933 0.0002513281797157498 -0.9551128980193431 -0.9127811121206568 0.8723771727888141
|
||||
126 -0.00017738706389382623 0.0008443302346762141 -0.0003895671701940069 -1.839402192955252 0.7766673236745506 0.7924995277225501
|
||||
127 -0.001000073944124535 0.0016468572053478946 -0.001033799846206151 0.08222028141230207 0.11760490751739432 1.8830161394199871
|
||||
128 0.0004239531801635865 0.0005168794447760295 -0.0008684808569629269 1.1686677946182742 -1.0381261833844448 0.31667529500400227
|
||||
129 -0.0004409215346868278 -0.001334846011966227 -0.0009927021813872098 -0.29452418106809986 -0.0931580604423265 -0.5695496505424753
|
||||
130 0.0010475849808729077 0.0006734593852494781 -0.000196916984145902 -0.049321887058332695 -2.9312636591061287 0.7616066487912013
|
||||
131 0.00038209178310713256 -0.0009628321808425074 -0.0013862456638785014 1.0492127631547312 0.1874792081286924 1.168765984508699
|
||||
132 0.0002998349801308538 0.0014133875635037733 0.0022406424034771963 0.575076201826299 0.5066190271889192 2.1361541858764506
|
||||
133 -0.00011535416048985546 -0.001041236448421046 0.0006208222935037978 0.32045995652530634 0.027939039439592323 0.021695984701765626
|
||||
134 -0.000987029914011318 0.0003500553257049557 -0.001043747540934093 1.4891578320741392 1.1151589305725869 0.24251250758555928
|
||||
135 -0.0007736630662934319 -0.000967059199293291 -0.0006397683905318742 -0.02417076632718488 1.5688231591106996 -0.4723484523158896
|
||||
136 0.0007295391299404002 0.00037747623153484286 0.0004510522053885847 1.9180704542629095 -0.23011140443522696 1.5192689109368365
|
||||
137 -3.411487464010032e-05 0.0005305965613622479 0.0011846926167481048 -1.0069971256282277 0.6425051512783104 -0.7900022519142518
|
||||
138 0.0001833854213995045 0.0011288904549903575 0.000308754866655325 1.0606136661717602 0.9017800698425885 -1.4181981833204758
|
||||
139 -0.0003669433422691092 -0.00028133432743200794 -0.0025213587271965365 0.6110684475733292 0.6766724972230532 -0.08234206862684952
|
||||
140 -0.0015131285007788794 -0.00047932227630192753 0.0003214665201627273 -0.6358611781374092 -1.6870181068210965 -0.781902178156614
|
||||
141 -0.0012436739915550252 -0.0009977354846392023 3.7112034981797074e-05 -0.6365194986922683 -0.30936951076225744 0.691170950137225
|
||||
142 0.0008904963121003822 -6.935173072402482e-05 -0.00019385497034208398 0.39875153999589447 0.1170376818780472 -0.3896029747301731
|
||||
143 -9.105595122636732e-05 0.0005154380348575327 0.0015000446982266441 -1.0666759832471555 0.21484194730690612 -0.9785005663759413
|
||||
144 -0.00022173918341567467 -0.0022834626691515727 0.00047409130709445837 0.40991111056117013 0.4170482715738036 -1.463544258074392
|
||||
145 0.0014087158997011032 0.000590985481235564 0.0008470107798063848 1.4059335910946213 -1.2396510038892823 -0.15776391781443064
|
||||
146 -0.0009109264393636273 0.00043064203581946086 -3.385101992955357e-05 -0.29248506567124016 0.13213896049033017 0.15248884930478313
|
||||
147 0.0008958257305797349 -0.00042544032979553904 0.0010693000057161858 0.5655696340306448 -0.004419562051025544 0.25329683367124206
|
||||
148 -0.0012244669175850524 0.0003777690850238906 -0.0005362154272677985 1.9878055073351206 0.18048094348117455 0.6092581911235572
|
||||
|
||||
Bonds
|
||||
|
||||
1 1 1 2
|
||||
2 1 74 1
|
||||
3 1 2 3
|
||||
4 1 3 4
|
||||
5 1 4 5
|
||||
6 1 5 6
|
||||
7 1 6 7
|
||||
8 1 7 8
|
||||
9 1 8 9
|
||||
10 1 9 10
|
||||
11 1 10 11
|
||||
12 1 11 12
|
||||
13 1 12 13
|
||||
14 1 13 14
|
||||
15 1 14 15
|
||||
16 1 15 16
|
||||
17 1 16 17
|
||||
18 1 17 18
|
||||
19 1 18 19
|
||||
20 1 19 20
|
||||
21 1 20 21
|
||||
22 1 21 22
|
||||
23 1 22 23
|
||||
24 1 23 24
|
||||
25 1 24 25
|
||||
26 1 25 26
|
||||
27 1 26 27
|
||||
28 1 27 28
|
||||
29 1 28 29
|
||||
30 1 29 30
|
||||
31 1 30 31
|
||||
32 1 31 32
|
||||
33 1 32 33
|
||||
34 1 33 34
|
||||
35 1 34 35
|
||||
36 1 35 36
|
||||
37 1 36 37
|
||||
38 1 37 38
|
||||
39 1 38 39
|
||||
40 1 39 40
|
||||
41 1 40 41
|
||||
42 1 41 42
|
||||
43 1 42 43
|
||||
44 1 43 44
|
||||
45 1 44 45
|
||||
46 1 45 46
|
||||
47 1 46 47
|
||||
48 1 47 48
|
||||
49 1 48 49
|
||||
50 1 49 50
|
||||
51 1 50 51
|
||||
52 1 51 52
|
||||
53 1 52 53
|
||||
54 1 53 54
|
||||
55 1 54 55
|
||||
56 1 55 56
|
||||
57 1 56 57
|
||||
58 1 57 58
|
||||
59 1 58 59
|
||||
60 1 59 60
|
||||
61 1 60 61
|
||||
62 1 61 62
|
||||
63 1 62 63
|
||||
64 1 63 64
|
||||
65 1 64 65
|
||||
66 1 65 66
|
||||
67 1 66 67
|
||||
68 1 67 68
|
||||
69 1 68 69
|
||||
70 1 69 70
|
||||
71 1 70 71
|
||||
72 1 71 72
|
||||
73 1 72 73
|
||||
74 1 73 74
|
||||
75 1 75 76
|
||||
76 1 148 75
|
||||
77 1 76 77
|
||||
78 1 77 78
|
||||
79 1 78 79
|
||||
80 1 79 80
|
||||
81 1 80 81
|
||||
82 1 81 82
|
||||
83 1 82 83
|
||||
84 1 83 84
|
||||
85 1 84 85
|
||||
86 1 85 86
|
||||
87 1 86 87
|
||||
88 1 87 88
|
||||
89 1 88 89
|
||||
90 1 89 90
|
||||
91 1 90 91
|
||||
92 1 91 92
|
||||
93 1 92 93
|
||||
94 1 93 94
|
||||
95 1 94 95
|
||||
96 1 95 96
|
||||
97 1 96 97
|
||||
98 1 97 98
|
||||
99 1 98 99
|
||||
100 1 99 100
|
||||
101 1 100 101
|
||||
102 1 101 102
|
||||
103 1 102 103
|
||||
104 1 103 104
|
||||
105 1 104 105
|
||||
106 1 105 106
|
||||
107 1 106 107
|
||||
108 1 107 108
|
||||
109 1 108 109
|
||||
110 1 109 110
|
||||
111 1 110 111
|
||||
112 1 111 112
|
||||
113 1 112 113
|
||||
114 1 113 114
|
||||
115 1 114 115
|
||||
116 1 115 116
|
||||
117 1 116 117
|
||||
118 1 117 118
|
||||
119 1 118 119
|
||||
120 1 119 120
|
||||
121 1 120 121
|
||||
122 1 121 122
|
||||
123 1 122 123
|
||||
124 1 123 124
|
||||
125 1 124 125
|
||||
126 1 125 126
|
||||
127 1 126 127
|
||||
128 1 127 128
|
||||
129 1 128 129
|
||||
130 1 129 130
|
||||
131 1 130 131
|
||||
132 1 131 132
|
||||
133 1 132 133
|
||||
134 1 133 134
|
||||
135 1 134 135
|
||||
136 1 135 136
|
||||
137 1 136 137
|
||||
138 1 137 138
|
||||
139 1 138 139
|
||||
140 1 139 140
|
||||
141 1 140 141
|
||||
142 1 141 142
|
||||
143 1 142 143
|
||||
144 1 143 144
|
||||
145 1 144 145
|
||||
146 1 145 146
|
||||
147 1 146 147
|
||||
148 1 147 148
|
||||
|
||||
Ellipsoids
|
||||
|
||||
1 9.999999997766462 9.999999997766462 9.999999997766462 0.9828541875306525 0.12879706731240614 -0.10093645894201106 0.08497524793392826
|
||||
2 9.999999997766462 9.999999997766462 9.999999997766462 0.9076319099077714 0.14371009860279324 -0.0061127301821370696 0.3943530882425885
|
||||
3 9.999999997766462 9.999999997766462 9.999999997766462 0.7156666230136304 0.13639947227633528 0.03941894579775276 0.6838586223622523
|
||||
4 9.999999997766462 9.999999997766462 9.999999997766462 0.551483876992997 0.0945081114480617 0.05507676463033448 0.826982648116119
|
||||
5 9.999999997766462 9.999999997766462 9.999999997766462 0.24878195093628586 0.25477295141293216 0.17560035853168876 0.9178032459085236
|
||||
6 9.999999997766462 9.999999997766462 9.999999997766462 -0.09814576590180418 0.2630252745002951 0.0750862666667879 0.9568422890777962
|
||||
7 9.999999997766462 9.999999997766462 9.999999997766462 -0.36099905322484027 0.20576958877633506 0.05427501922331751 0.9079607822994866
|
||||
8 9.999999997766462 9.999999997766462 9.999999997766462 -0.7222470672351088 0.18134561062508855 -0.07603445152283007 0.6630925316718025
|
||||
9 9.999999997766462 9.999999997766462 9.999999997766462 0.7207213859113211 -0.081618921713485 0.2444656792207328 -0.6435336566113217
|
||||
10 9.999999997766462 9.999999997766462 9.999999997766462 0.9121007124750514 -0.01217119606138896 0.2913039145765659 -0.2882120428457281
|
||||
11 9.999999997766462 9.999999997766462 9.999999997766462 0.953249593652999 0.05081512321641071 0.29695596119287027 -0.0234561839375449
|
||||
12 9.999999997766462 9.999999997766462 9.999999997766462 0.893216854716605 0.19782387032700505 0.32197381347668597 0.2436436541638224
|
||||
13 9.999999997766462 9.999999997766462 9.999999997766462 0.7804220903358083 0.3075288797089802 0.40715287039611386 0.3613777652111879
|
||||
14 9.999999997766462 9.999999997766462 9.999999997766462 0.6203605365073518 0.3741569541553062 0.35408302093722205 0.5914258978819795
|
||||
15 9.999999997766462 9.999999997766462 9.999999997766462 0.3960444020645081 0.5102735688288697 0.4358052977828721 0.6267722544691949
|
||||
16 9.999999997766462 9.999999997766462 9.999999997766462 0.13777757932263526 0.6041124653901045 0.23900745590897193 0.7476235040554876
|
||||
17 9.999999997766462 9.999999997766462 9.999999997766462 -0.14487300744864823 0.6140449381421356 0.15150134965763856 0.7609257300858729
|
||||
18 9.999999997766462 9.999999997766462 9.999999997766462 -0.3344250731601342 0.6010892081702673 -0.017846433649279014 0.7256260325188738
|
||||
19 9.999999997766462 9.999999997766462 9.999999997766462 -0.5074640025256208 0.5175428589716987 -0.22947810189520476 0.6495917764401355
|
||||
20 9.999999997766462 9.999999997766462 9.999999997766462 0.6927772486705646 -0.40626836540518185 0.4423107744840648 -0.3992078127626656
|
||||
21 9.999999997766462 9.999999997766462 9.999999997766462 0.6829206576647326 -0.27522098535816325 0.6168603801346256 -0.27812956688100604
|
||||
22 9.999999997766462 9.999999997766462 9.999999997766462 0.6788549938954256 0.033964180979933575 0.7308067787169422 -0.06264011378478199
|
||||
23 9.999999997766462 9.999999997766462 9.999999997766462 0.5999805514844269 0.2793954015736318 0.7386615340865574 0.12783069068438008
|
||||
24 9.999999997766462 9.999999997766462 9.999999997766462 0.4418314756383255 0.5057611588638139 0.7228215888566917 0.16284823610552174
|
||||
25 9.999999997766462 9.999999997766462 9.999999997766462 0.3141779374831782 0.7142758691047312 0.539765722838384 0.31584041993110096
|
||||
26 9.999999997766462 9.999999997766462 9.999999997766462 0.13009402904433304 0.8026224209437359 0.4188011593597563 0.40432459970221063
|
||||
27 9.999999997766462 9.999999997766462 9.999999997766462 0.015395939306808548 0.9125609417624169 0.11793521250895517 0.3912630550831749
|
||||
28 9.999999997766462 9.999999997766462 9.999999997766462 0.020389821926513313 0.8930600411816652 -0.2308403071738297 0.3856692502524667
|
||||
29 9.999999997766462 9.999999997766462 9.999999997766462 -0.19829980450156168 0.789544960878009 -0.45297996531610585 0.3634626436224299
|
||||
30 9.999999997766462 9.999999997766462 9.999999997766462 -0.29878991597718874 0.6265110900381559 -0.6619230912649768 0.28295982297804007
|
||||
31 9.999999997766462 9.999999997766462 9.999999997766462 0.3240360642338418 -0.36827828790860756 0.8343565738846102 -0.2514375456181544
|
||||
32 9.999999997766462 9.999999997766462 9.999999997766462 0.32014650617553997 -0.05971181117410955 0.9438400245399936 -0.05573797867026355
|
||||
33 9.999999997766462 9.999999997766462 9.999999997766462 0.24982350857997523 0.1590081591159326 0.9549704885538687 -0.01832991779955874
|
||||
34 9.999999997766462 9.999999997766462 9.999999997766462 0.16999266129422064 0.3749550480019231 0.9099327896340427 -0.05033413784692161
|
||||
35 9.999999997766462 9.999999997766462 9.999999997766462 0.19340334476340248 0.6890998585251199 0.6972337573677242 0.040020229907810456
|
||||
36 9.999999997766462 9.999999997766462 9.999999997766462 0.1612116171856501 0.859720290458655 0.48091314403740787 0.06011975174706676
|
||||
37 9.999999997766462 9.999999997766462 9.999999997766462 0.009261495255550381 0.9402304673687385 0.3245385528799807 0.10274055008497525
|
||||
38 9.999999997766462 9.999999997766462 9.999999997766462 -0.178489162453817 0.9806521854786103 0.005310303981292909 0.08021664836046656
|
||||
39 9.999999997766462 9.999999997766462 9.999999997766462 -0.1288029405461015 0.9602840555925231 -0.21902557887358792 0.11529150393911712
|
||||
40 9.999999997766462 9.999999997766462 9.999999997766462 -0.04731791323035676 0.8474709401996229 -0.5273646012711862 0.037955209534064525
|
||||
41 9.999999997766462 9.999999997766462 9.999999997766462 -0.022651622917573347 0.5565011565487459 -0.8295791934725275 -0.03989647223225978
|
||||
42 9.999999997766462 9.999999997766462 9.999999997766462 -0.13596774829773478 -0.40509299019424533 0.9040951590175422 0.004938031933284807
|
||||
43 9.999999997766462 9.999999997766462 9.999999997766462 -0.23079724764482035 -0.14600108158768343 0.957686102648897 -0.09084956492998986
|
||||
44 9.999999997766462 9.999999997766462 9.999999997766462 -0.24753675871742536 0.17224891940889686 0.9383869011016502 -0.16877762495953091
|
||||
45 9.999999997766462 9.999999997766462 9.999999997766462 -0.2811167754571826 0.35162969585761844 0.8297679896375197 -0.32987118534443655
|
||||
46 9.999999997766462 9.999999997766462 9.999999997766462 -0.26615049812015845 0.5992229988318759 0.625822287547174 -0.422424164117712
|
||||
47 9.999999997766462 9.999999997766462 9.999999997766462 -0.26520515010155843 0.7417880533852412 0.3692915113072771 -0.49299137101062096
|
||||
48 9.999999997766462 9.999999997766462 9.999999997766462 -0.16226711788695447 0.8323801954647086 0.1174686480853541 -0.5167336928900556
|
||||
49 9.999999997766462 9.999999997766462 9.999999997766462 -0.04572661296718043 0.8408693531665875 -0.11047316886003926 -0.5278669214241181
|
||||
50 9.999999997766462 9.999999997766462 9.999999997766462 0.19411685314820926 0.7587839226558699 -0.3585937241690634 -0.5079135231802451
|
||||
51 9.999999997766462 9.999999997766462 9.999999997766462 0.2884389061686524 0.6577064384331197 -0.5877305498173151 -0.3725560884796933
|
||||
52 9.999999997766462 9.999999997766462 9.999999997766462 -0.40417504294512524 -0.5007922981141542 0.722387900683145 0.2529927464502668
|
||||
53 9.999999997766462 9.999999997766462 9.999999997766462 0.487705221455796 0.2123778745642691 -0.8387806766732518 -0.11613023637226708
|
||||
54 9.999999997766462 9.999999997766462 9.999999997766462 0.6413097692721371 -0.008544696549571698 -0.7672266752769908 0.0034636311017504627
|
||||
55 9.999999997766462 9.999999997766462 9.999999997766462 0.6030429100152689 -0.25373110064689114 -0.7459977158111821 0.12428670584311194
|
||||
56 9.999999997766462 9.999999997766462 9.999999997766462 0.5864519496083405 -0.372875091537276 -0.6178931881796406 0.36775846001532553
|
||||
57 9.999999997766462 9.999999997766462 9.999999997766462 -0.48911574896863785 0.5441144354000708 0.4276113192775303 -0.5308990722593522
|
||||
58 9.999999997766462 9.999999997766462 9.999999997766462 -0.4417465957365199 0.6181565224178451 0.16076362948117487 -0.6299980272854125
|
||||
59 9.999999997766462 9.999999997766462 9.999999997766462 -0.28308904114546696 0.6664475020761871 -0.017606380786631723 -0.6894913611607815
|
||||
60 9.999999997766462 9.999999997766462 9.999999997766462 -0.04343392830476409 0.6249932397866798 -0.2350918967721212 -0.7431209485440797
|
||||
61 9.999999997766462 9.999999997766462 9.999999997766462 0.3001051086276221 0.5396150277384395 -0.35255590439280615 -0.7031762793867672
|
||||
62 9.999999997766462 9.999999997766462 9.999999997766462 0.556986262583898 0.4368102678055262 -0.5133240400778073 -0.4852437769932583
|
||||
63 9.999999997766462 9.999999997766462 9.999999997766462 0.795279938190695 0.19986687104396691 -0.4327075609483636 -0.3746294442093639
|
||||
64 9.999999997766462 9.999999997766462 9.999999997766462 0.8774746414896595 0.14848167889587988 -0.4429894517950587 -0.10840567408197696
|
||||
65 9.999999997766462 9.999999997766462 9.999999997766462 0.9026256675673767 0.09862023274988396 -0.3935312309258709 0.14378499305169315
|
||||
66 9.999999997766462 9.999999997766462 9.999999997766462 0.7992966483039178 0.0008565776883433751 -0.3722117248777941 0.4717865684271695
|
||||
67 9.999999997766462 9.999999997766462 9.999999997766462 0.5936072962961377 -0.03652051284490529 -0.2825637892972656 0.7526316063676206
|
||||
68 9.999999997766462 9.999999997766462 9.999999997766462 0.43644057731838104 -0.13786664664361545 -0.15590190259912107 0.8753325122370452
|
||||
69 9.999999997766462 9.999999997766462 9.999999997766462 0.14188152802643034 -0.12788407699426005 0.012864675110957144 0.9815038435943596
|
||||
70 9.999999997766462 9.999999997766462 9.999999997766462 -0.17011699210314196 -0.1964455848932923 0.08682166929707971 0.9617335072223387
|
||||
71 9.999999997766462 9.999999997766462 9.999999997766462 -0.38329053167753524 -0.1996467474595419 0.09852206601835616 0.8963944148992972
|
||||
72 9.999999997766462 9.999999997766462 9.999999997766462 0.6594122085000511 0.160793297137392 -0.16758115116995345 -0.7150088199800926
|
||||
73 9.999999997766462 9.999999997766462 9.999999997766462 0.8512883171626583 0.18060232735097068 -0.17245589356555377 -0.4614650205511664
|
||||
74 9.999999997766462 9.999999997766462 9.999999997766462 0.9616314641817232 0.12709468738918034 -0.12391907222748418 -0.20917918412557554
|
||||
75 9.999999997766462 9.999999997766462 9.999999997766462 0.11151873278872049 0.1669724888151189 0.9775349714635312 -0.06410257234991716
|
||||
76 9.999999997766462 9.999999997766462 9.999999997766462 0.002211126817898623 0.5521186363105357 0.8337434054774612 0.0056618176970950045
|
||||
77 9.999999997766462 9.999999997766462 9.999999997766462 0.07044943717430134 0.7729866626831493 0.6298061627604926 0.029541385625851832
|
||||
78 9.999999997766462 9.999999997766462 9.999999997766462 -0.010806653246459833 0.9027252443710524 0.411417996086784 0.1253219131547623
|
||||
79 9.999999997766462 9.999999997766462 9.999999997766462 -0.06940131778729772 0.9746360030066041 0.11360573819677272 0.17989401041019523
|
||||
80 9.999999997766462 9.999999997766462 9.999999997766462 -0.20000556212707324 0.9595560965524266 -0.15823100448109342 0.11921754027075034
|
||||
81 9.999999997766462 9.999999997766462 9.999999997766462 -0.26251769804085484 0.8226181738157728 -0.4903553171765896 0.11804855458657725
|
||||
82 9.999999997766462 9.999999997766462 9.999999997766462 -0.3837234853374367 0.6543399037804607 -0.6234720263018537 0.1894154416623109
|
||||
83 9.999999997766462 9.999999997766462 9.999999997766462 0.3855852781915845 -0.47229630772423525 0.7839693435947087 -0.11684288277706342
|
||||
84 9.999999997766462 9.999999997766462 9.999999997766462 0.46002037442553534 -0.1407678919113547 0.866403276034954 -0.1338320551890411
|
||||
85 9.999999997766462 9.999999997766462 9.999999997766462 0.48887603366012683 0.1731127982177676 0.8530376609375365 0.05795629239499309
|
||||
86 9.999999997766462 9.999999997766462 9.999999997766462 0.43899101160689896 0.3758967470065976 0.8089928976311329 0.1073266923956608
|
||||
87 9.999999997766462 9.999999997766462 9.999999997766462 0.3553143558383719 0.6425723574078863 0.5903209324805503 0.33522182313466425
|
||||
88 9.999999997766462 9.999999997766462 9.999999997766462 0.2536540111199051 0.7421214888111948 0.45155240831127663 0.42545947049716176
|
||||
89 9.999999997766462 9.999999997766462 9.999999997766462 0.15382396432141013 0.7505310904822217 0.14263847154124493 0.6266542401168209
|
||||
90 9.999999997766462 9.999999997766462 9.999999997766462 -0.16810175118036055 0.7288374808427736 -0.10080598156099228 0.6560303970475613
|
||||
91 9.999999997766462 9.999999997766462 9.999999997766462 -0.2831885739735942 0.643948067209743 -0.26839675685463915 0.6581020431646983
|
||||
92 9.999999997766462 9.999999997766462 9.999999997766462 -0.4831024117054533 0.453267716115057 -0.42739397992663336 0.6152193293896797
|
||||
93 9.999999997766462 9.999999997766462 9.999999997766462 0.6770118192914993 -0.21059755897505428 0.4910911741276808 -0.5060959626269103
|
||||
94 9.999999997766462 9.999999997766462 9.999999997766462 0.7442670171743097 -0.08947621534664056 0.6143775419962679 -0.2461723987865454
|
||||
95 9.999999997766462 9.999999997766462 9.999999997766462 0.7666665318729418 0.12269014310665635 0.6290675727017766 -0.03799403460385277
|
||||
96 9.999999997766462 9.999999997766462 9.999999997766462 0.7171919647397696 0.27392119614493066 0.6165739462155079 0.17446900258634976
|
||||
97 9.999999997766462 9.999999997766462 9.999999997766462 0.6242311603419127 0.43977982483754113 0.46478542263682826 0.4482227961944326
|
||||
98 9.999999997766462 9.999999997766462 9.999999997766462 0.42790222650129595 0.5250655697375166 0.4214312365282337 0.6029938183014272
|
||||
99 9.999999997766462 9.999999997766462 9.999999997766462 0.2468582232791126 0.49224626821105333 0.30309532857077576 0.7777453637472519
|
||||
100 9.999999997766462 9.999999997766462 9.999999997766462 -0.03380456035420594 0.5634460183047242 0.08545990308043122 0.8210252378101995
|
||||
101 9.999999997766462 9.999999997766462 9.999999997766462 -0.26750916515001516 0.4857064004847054 0.009320517332115886 0.8321305588942125
|
||||
102 9.999999997766462 9.999999997766462 9.999999997766462 -0.543656333310932 0.3668193234682623 -0.09381801460790738 0.7490524382953638
|
||||
103 9.999999997766462 9.999999997766462 9.999999997766462 0.7108784431095552 -0.3004632412363646 0.2190205688208185 -0.5969955361820375
|
||||
104 9.999999997766462 9.999999997766462 9.999999997766462 0.8734231811131953 -0.14399683070372168 0.19737468070828412 -0.4212363883340244
|
||||
105 9.999999997766462 9.999999997766462 9.999999997766462 0.9684624161954964 -0.105190045875246 0.17391545136610614 -0.14411460176424984
|
||||
106 9.999999997766462 9.999999997766462 9.999999997766462 0.9799304485597246 0.037984124779449666 0.14105544742949488 0.13563510976418097
|
||||
107 9.999999997766462 9.999999997766462 9.999999997766462 0.8816175546504624 0.20405639480623733 0.14071717244217888 0.40163435168159917
|
||||
108 9.999999997766462 9.999999997766462 9.999999997766462 0.6668815181201708 0.2184913756962591 0.13935946384415568 0.6986483374152993
|
||||
109 9.999999997766462 9.999999997766462 9.999999997766462 0.49523667831069 0.06959764035843413 0.04878276823652622 0.8645906791282876
|
||||
110 9.999999997766462 9.999999997766462 9.999999997766462 0.2207732329238526 -0.06373893139772668 0.037699540120053256 0.9725097803741426
|
||||
111 9.999999997766462 9.999999997766462 9.999999997766462 -0.032729617987676665 -0.18237738709355036 0.08976233597699147 0.9785754870337106
|
||||
112 9.999999997766462 9.999999997766462 9.999999997766462 -0.15032793635914565 -0.23367266896015637 0.20496632388946223 0.9385027444830824
|
||||
113 9.999999997766462 9.999999997766462 9.999999997766462 0.5098818708103572 0.17022830741237596 -0.2655328085989286 -0.8003343855739379
|
||||
114 9.999999997766462 9.999999997766462 9.999999997766462 0.7386002630722802 0.13150233806957554 -0.2899184849443961 -0.5942424240655826
|
||||
115 9.999999997766462 9.999999997766462 9.999999997766462 0.8183885516845668 0.21176889551544467 -0.29030250974778893 -0.44846244680902864
|
||||
116 9.999999997766462 9.999999997766462 9.999999997766462 0.9430612626489262 0.10580295822334976 -0.2990836107868347 -0.09995090135116472
|
||||
117 9.999999997766462 9.999999997766462 9.999999997766462 0.9613379941508746 0.03141943836189481 -0.22153618567675704 0.16051105360936818
|
||||
118 9.999999997766462 9.999999997766462 9.999999997766462 0.8625667911488177 0.009442517727487543 -0.19942173035959687 0.46488745210704746
|
||||
119 9.999999997766462 9.999999997766462 9.999999997766462 0.7259073589630057 -0.13376476050843852 -0.17209740381142 0.6523403855740064
|
||||
120 9.999999997766462 9.999999997766462 9.999999997766462 0.5281310594886722 -0.2846679630342966 -0.07506778574311505 0.7964964296021063
|
||||
121 9.999999997766462 9.999999997766462 9.999999997766462 0.24241907358145395 -0.3683073657243024 0.039055584363879806 0.8966924436210727
|
||||
122 9.999999997766462 9.999999997766462 9.999999997766462 -0.044981165612273756 -0.40529534424684105 0.1971478516389492 0.8915408589998233
|
||||
123 9.999999997766462 9.999999997766462 9.999999997766462 -0.3495232584251298 -0.40209106895373176 0.34714827984449365 0.7717799789373487
|
||||
124 9.999999997766462 9.999999997766462 9.999999997766462 0.5344020410886484 0.3826673897545711 -0.38492167218812157 -0.6479316581080214
|
||||
125 9.999999997766462 9.999999997766462 9.999999997766462 0.7053269695515239 0.29260497262472956 -0.500965349977395 -0.40734495718073077
|
||||
126 9.999999997766462 9.999999997766462 9.999999997766462 0.7696439701870998 0.21424045744249637 -0.5824916559487316 -0.1498421045620125
|
||||
127 9.999999997766462 9.999999997766462 9.999999997766462 0.7423816103336222 0.1139330316098165 -0.6216492250908265 0.22235343462746351
|
||||
128 9.999999997766462 9.999999997766462 9.999999997766462 0.5887700508646756 -0.08843642096111673 -0.6840133892265956 0.4214908184185525
|
||||
129 9.999999997766462 9.999999997766462 9.999999997766462 0.453096146271983 -0.38728607571982976 -0.6241259420947486 0.5051536263270361
|
||||
130 9.999999997766462 9.999999997766462 9.999999997766462 -0.4409693358675804 0.53279196704852 0.4417418096721996 -0.5714393565905346
|
||||
131 9.999999997766462 9.999999997766462 9.999999997766462 -0.18566644236274712 0.6770317752573873 0.25184635469644123 -0.6661301382600142
|
||||
132 9.999999997766462 9.999999997766462 9.999999997766462 0.015608637060561658 0.7425789407541207 -0.020406929491472138 -0.6692656008090734
|
||||
133 9.999999997766462 9.999999997766462 9.999999997766462 0.08018393872270876 0.7828265827838332 -0.23834222384166942 -0.5691625967964753
|
||||
134 9.999999997766462 9.999999997766462 9.999999997766462 0.13194668226893702 0.7589329168513657 -0.46681103776605365 -0.43439424003717964
|
||||
135 9.999999997766462 9.999999997766462 9.999999997766462 0.23078479216727615 0.7124321296591045 -0.5847273355040361 -0.31188585002858094
|
||||
136 9.999999997766462 9.999999997766462 9.999999997766462 -0.25136284638005546 -0.45701375225575186 0.841389844073701 0.14148597103058816
|
||||
137 9.999999997766462 9.999999997766462 9.999999997766462 -0.33882629405552384 -0.365928882584538 0.8652581637618377 0.05119673222505744
|
||||
138 9.999999997766462 9.999999997766462 9.999999997766462 -0.3901032217728516 -0.04271905647523107 0.919195929073709 -0.03276282269018462
|
||||
139 9.999999997766462 9.999999997766462 9.999999997766462 -0.3503464321192356 0.2164507057056595 0.8846466649907219 -0.21864754199770353
|
||||
140 9.999999997766462 9.999999997766462 9.999999997766462 -0.2714234139641493 0.5100075547669219 0.7525252671110235 -0.3161128703362045
|
||||
141 9.999999997766462 9.999999997766462 9.999999997766462 -0.18623801902606954 0.7425995746707363 0.5393607888180064 -0.35064399531961904
|
||||
142 9.999999997766462 9.999999997766462 9.999999997766462 -0.20986530401416495 0.8687694482447833 0.31310815046609125 -0.3211845047308489
|
||||
143 9.999999997766462 9.999999997766462 9.999999997766462 -0.1354858154681459 0.9418151150282347 0.014007263864675714 -0.3072973795370049
|
||||
144 9.999999997766462 9.999999997766462 9.999999997766462 -0.09121534676964865 0.942226022288734 -0.27543028841845296 -0.16741576884323378
|
||||
145 9.999999997766462 9.999999997766462 9.999999997766462 -0.07761809459687324 0.8625267258049417 -0.49537475942792236 -0.06802151413402847
|
||||
146 9.999999997766462 9.999999997766462 9.999999997766462 -0.07853628249634757 0.6763776292711046 -0.7295609015799718 -0.06392375019562685
|
||||
147 9.999999997766462 9.999999997766462 9.999999997766462 0.18414802295685903 -0.34920401662445405 0.9187682994180332 0.0032973320918147885
|
||||
148 9.999999997766462 9.999999997766462 9.999999997766462 0.13019081328575915 -0.1370605858009623 0.9781659097238085 -0.08634929652338917
|
||||
@ -0,0 +1,73 @@
|
||||
# LAMMPS input file in real units via oxdna lj2real.py, date 2024-05-19
|
||||
variable number equal 5
|
||||
variable ofreq equal 1000
|
||||
variable efreq equal 1000
|
||||
variable T equal 300.0
|
||||
variable rhos equal 0.2
|
||||
|
||||
units real
|
||||
|
||||
dimension 3
|
||||
|
||||
newton on
|
||||
|
||||
boundary p p p
|
||||
|
||||
atom_style hybrid bond ellipsoid oxdna
|
||||
atom_modify sort 0 8.518
|
||||
|
||||
# Pair interactions require lists of neighbours to be calculated
|
||||
neighbor 17.036 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
read_data data.dsring
|
||||
|
||||
set atom * mass 315.8376
|
||||
|
||||
group all type 1 4
|
||||
|
||||
# oxDNA2 bond interactions - FENE backbone
|
||||
bond_style oxdna2/fene
|
||||
bond_coeff * 11.92337812042065 2.1295 6.4430152
|
||||
special_bonds lj 0 1 1
|
||||
|
||||
# oxDNA2 pair interactions
|
||||
pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
|
||||
pair_coeff * * oxdna2/excv 11.92337812042065 5.9626 5.74965 11.92337812042065 4.38677 4.259 11.92337812042065 2.81094 2.72576
|
||||
pair_coeff * * oxdna2/stk seqdep ${T} 8.06199211612242 0.005309213 0.70439070204273 3.4072 7.6662 2.72576 6.3885 1.3 0.0 0.8 0.9 0.0 0.95 0.9 0.0 0.95 2.0 0.65 2.0 0.65
|
||||
pair_coeff * * oxdna2/hbond seqdep 0.0 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0.0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45
|
||||
pair_coeff 1 4 oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45
|
||||
pair_coeff 2 3 oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45
|
||||
pair_coeff * * oxdna2/xstk 3.9029021145006 4.89785 5.74965 4.21641 5.57929 2.25 0.791592654 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
|
||||
pair_coeff * * oxdna2/coaxstk 4.80673207785863 3.4072 5.1108 1.87396 4.94044 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793
|
||||
pair_coeff * * oxdna2/dh ${T} ${rhos} 0.815
|
||||
|
||||
# NVE ensemble
|
||||
fix 1 all nve/asphere
|
||||
#fix 2 all langevin ${T} ${T} 4265.0 457145 angmom 10
|
||||
|
||||
timestep 0.01706
|
||||
|
||||
#comm_style tiled
|
||||
fix 3 all balance 1000 1.03 shift xyz 10 1.03
|
||||
comm_modify cutoff 32.4
|
||||
|
||||
compute quat all property/atom quatw quati quatj quatk
|
||||
|
||||
compute erot all erotate/asphere
|
||||
compute ekin all ke
|
||||
compute epot all pe
|
||||
variable erot equal c_erot
|
||||
variable ekin equal c_ekin
|
||||
variable epot equal c_epot
|
||||
variable etot equal c_erot+c_ekin+c_epot
|
||||
fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
|
||||
|
||||
dump out all custom ${ofreq} out.${number}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz
|
||||
dump_modify out sort id
|
||||
dump_modify out format line "%d %d %d %22.15le %22.15le %22.15le %d %d %d %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le"
|
||||
|
||||
run 100000
|
||||
|
||||
write_data last_config.${number}.* nocoeff
|
||||
#write_restart last_config.${number}.*
|
||||
@ -0,0 +1,286 @@
|
||||
LAMMPS (17 Apr 2024 - Development - patch_17Apr2024-174-g749e259294-modified)
|
||||
# LAMMPS input file in real units via oxdna lj2real.py, date 2024-05-19
|
||||
variable number equal 5
|
||||
variable ofreq equal 1000
|
||||
variable efreq equal 1000
|
||||
variable T equal 300.0
|
||||
variable rhos equal 0.2
|
||||
|
||||
units real
|
||||
|
||||
dimension 3
|
||||
|
||||
newton on
|
||||
|
||||
boundary p p p
|
||||
|
||||
atom_style hybrid bond ellipsoid oxdna
|
||||
WARNING: Atom style hybrid defines both, per-type and per-atom masses; both must be set, but only per-atom masses will be used (../atom_vec_hybrid.cpp:132)
|
||||
atom_modify sort 0 8.518
|
||||
|
||||
# Pair interactions require lists of neighbours to be calculated
|
||||
neighbor 17.036 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
read_data data.dsring
|
||||
Reading data file ...
|
||||
orthogonal box = (0 0 0) to (851 851 851)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
148 atoms
|
||||
reading velocities ...
|
||||
148 velocities
|
||||
scanning bonds ...
|
||||
1 = max bonds/atom
|
||||
148 ellipsoids
|
||||
orthogonal box = (0 0 0) to (851 851 851)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading bonds ...
|
||||
148 bonds
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 0 0
|
||||
special bond factors coul: 0 0 0
|
||||
2 = max # of 1-2 neighbors
|
||||
2 = max # of 1-3 neighbors
|
||||
4 = max # of 1-4 neighbors
|
||||
6 = max # of special neighbors
|
||||
special bonds CPU = 0.000 seconds
|
||||
read_data CPU = 0.012 seconds
|
||||
|
||||
set atom * mass 315.8376
|
||||
Setting atom values ...
|
||||
148 settings made for mass
|
||||
|
||||
group all type 1 4
|
||||
148 atoms in group all
|
||||
|
||||
# oxDNA2 bond interactions - FENE backbone
|
||||
bond_style oxdna2/fene
|
||||
bond_coeff * 11.92337812042065 2.1295 6.4430152
|
||||
special_bonds lj 0 1 1
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 1 1
|
||||
special bond factors coul: 0 0 0
|
||||
2 = max # of 1-2 neighbors
|
||||
2 = max # of 1-3 neighbors
|
||||
4 = max # of 1-4 neighbors
|
||||
6 = max # of special neighbors
|
||||
special bonds CPU = 0.000 seconds
|
||||
|
||||
# oxDNA2 pair interactions
|
||||
pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
|
||||
pair_coeff * * oxdna2/excv 11.92337812042065 5.9626 5.74965 11.92337812042065 4.38677 4.259 11.92337812042065 2.81094 2.72576
|
||||
pair_coeff * * oxdna2/stk seqdep ${T} 8.06199211612242 0.005309213 0.70439070204273 3.4072 7.6662 2.72576 6.3885 1.3 0.0 0.8 0.9 0.0 0.95 0.9 0.0 0.95 2.0 0.65 2.0 0.65
|
||||
pair_coeff * * oxdna2/stk seqdep 300 8.06199211612242 0.005309213 0.70439070204273 3.4072 7.6662 2.72576 6.3885 1.3 0.0 0.8 0.9 0.0 0.95 0.9 0.0 0.95 2.0 0.65 2.0 0.65
|
||||
pair_coeff * * oxdna2/hbond seqdep 0.0 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0.0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45
|
||||
pair_coeff 1 4 oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45
|
||||
pair_coeff 2 3 oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45
|
||||
pair_coeff * * oxdna2/xstk 3.9029021145006 4.89785 5.74965 4.21641 5.57929 2.25 0.791592654 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
|
||||
pair_coeff * * oxdna2/coaxstk 4.80673207785863 3.4072 5.1108 1.87396 4.94044 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793
|
||||
pair_coeff * * oxdna2/dh ${T} ${rhos} 0.815
|
||||
pair_coeff * * oxdna2/dh 300 ${rhos} 0.815
|
||||
pair_coeff * * oxdna2/dh 300 0.2 0.815
|
||||
|
||||
# NVE ensemble
|
||||
fix 1 all nve/asphere
|
||||
#fix 2 all langevin ${T} ${T} 4265.0 457145 angmom 10
|
||||
|
||||
timestep 0.01706
|
||||
|
||||
#comm_style tiled
|
||||
fix 3 all balance 1000 1.03 shift xyz 10 1.03
|
||||
comm_modify cutoff 32.4
|
||||
|
||||
compute quat all property/atom quatw quati quatj quatk
|
||||
|
||||
compute erot all erotate/asphere
|
||||
compute ekin all ke
|
||||
compute epot all pe
|
||||
variable erot equal c_erot
|
||||
variable ekin equal c_ekin
|
||||
variable epot equal c_epot
|
||||
variable etot equal c_erot+c_ekin+c_epot
|
||||
fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
|
||||
fix 5 all print 1000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
|
||||
|
||||
dump out all custom ${ofreq} out.${number}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz
|
||||
dump out all custom 1000 out.${number}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz
|
||||
dump out all custom 1000 out.5.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz
|
||||
dump_modify out sort id
|
||||
dump_modify out format line "%d %d %d %22.15le %22.15le %22.15le %d %d %d %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le"
|
||||
|
||||
run 100000
|
||||
Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 0 steps, check = yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 48.032697
|
||||
ghost atom cutoff = 48.032697
|
||||
binsize = 24.016348, bins = 36 36 36
|
||||
5 neighbor lists, perpetual/occasional/extra = 5 0 0
|
||||
(1) pair oxdna2/excv, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
(2) pair oxdna2/hbond, perpetual, copy from (1)
|
||||
attributes: half, newton on
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(3) pair oxdna2/xstk, perpetual, copy from (1)
|
||||
attributes: half, newton on
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(4) pair oxdna2/coaxstk, perpetual, copy from (1)
|
||||
attributes: half, newton on
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(5) pair oxdna2/dh, perpetual, copy from (1)
|
||||
attributes: half, newton on
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
WARNING: Communication cutoff adjusted to 48.03269686950012 (../comm.cpp:739)
|
||||
0 ekin = 122.015812851425 | erot = 125.402528675609 | epot = -1325.18559882055 | etot = -1077.76725729351
|
||||
Per MPI rank memory allocation (min/avg/max) = 7.806 | 7.806 | 7.806 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press Volume
|
||||
0 278.46107 -1367.7166 42.531022 -1203.1698 -0.0059756093 6.1629505e+08
|
||||
1000 ekin = 122.370905858635 | erot = 126.447129514011 | epot = -1326.58529267981 | etot = -1077.76725730717
|
||||
2000 ekin = 122.691275133791 | erot = 127.497291822809 | epot = -1327.95582427469 | etot = -1077.76725731809
|
||||
3000 ekin = 122.920677842253 | erot = 128.459039892254 | epot = -1329.14697506148 | etot = -1077.76725732698
|
||||
4000 ekin = 123.015104309575 | erot = 129.250631266888 | epot = -1330.03299290867 | etot = -1077.76725733221
|
||||
5000 ekin = 122.9570060981 | erot = 129.822304188926 | epot = -1330.54656761964 | etot = -1077.76725733262
|
||||
6000 ekin = 122.758396503728 | erot = 130.158463496347 | epot = -1330.68411732949 | etot = -1077.76725732941
|
||||
7000 ekin = 122.444997038107 | erot = 130.2721351435 | epot = -1330.48438950495 | etot = -1077.76725732334
|
||||
8000 ekin = 122.055455926322 | erot = 130.202756105441 | epot = -1330.02546934809 | etot = -1077.76725731633
|
||||
9000 ekin = 121.639778047767 | erot = 130.001921534636 | epot = -1329.40895689073 | etot = -1077.76725730833
|
||||
10000 ekin = 121.255561480542 | erot = 129.724613334693 | epot = -1328.74743211587 | etot = -1077.76725730064
|
||||
11000 ekin = 120.959150047792 | erot = 129.417382591736 | epot = -1328.14378993383 | etot = -1077.7672572943
|
||||
12000 ekin = 120.804873255896 | erot = 129.110119861451 | epot = -1327.68225040707 | etot = -1077.76725728973
|
||||
13000 ekin = 120.84692312026 | erot = 128.811452781899 | epot = -1327.42563318933 | etot = -1077.76725728717
|
||||
14000 ekin = 121.124227416954 | erot = 128.510318857508 | epot = -1327.40180356072 | etot = -1077.76725728626
|
||||
15000 ekin = 121.666723735015 | erot = 128.179805529182 | epot = -1327.61378655278 | etot = -1077.76725728858
|
||||
16000 ekin = 122.48420413773 | erot = 127.7714101238 | epot = -1328.02287155596 | etot = -1077.76725729443
|
||||
17000 ekin = 123.554901437623 | erot = 127.223257664149 | epot = -1328.54541640317 | etot = -1077.7672573014
|
||||
18000 ekin = 124.838358543238 | erot = 126.479155255363 | epot = -1329.0847711071 | etot = -1077.7672573085
|
||||
19000 ekin = 126.271030938727 | erot = 125.497490625599 | epot = -1329.5357788797 | etot = -1077.76725731537
|
||||
20000 ekin = 127.785246119996 | erot = 124.269691231027 | epot = -1329.82219466647 | etot = -1077.76725731544
|
||||
21000 ekin = 129.341920134184 | erot = 122.835059904168 | epot = -1329.94423735083 | etot = -1077.76725731248
|
||||
22000 ekin = 130.919691006211 | erot = 121.262876727301 | epot = -1329.94982504099 | etot = -1077.76725730747
|
||||
23000 ekin = 132.5067055481 | erot = 119.63798200526 | epot = -1329.91194485558 | etot = -1077.76725730222
|
||||
24000 ekin = 134.092490326559 | erot = 118.03901918442 | epot = -1329.8987668112 | etot = -1077.76725730022
|
||||
25000 ekin = 135.660464836621 | erot = 116.515685186215 | epot = -1329.94340732287 | etot = -1077.76725730004
|
||||
26000 ekin = 137.186778726604 | erot = 115.085213344397 | epot = -1330.03924937555 | etot = -1077.76725730455
|
||||
27000 ekin = 138.631216641226 | erot = 113.733576310579 | epot = -1330.13205025948 | etot = -1077.76725730768
|
||||
28000 ekin = 139.956351860934 | erot = 112.450817889846 | epot = -1330.17442705975 | etot = -1077.76725730897
|
||||
29000 ekin = 141.132095730945 | erot = 111.248013058276 | epot = -1330.14736609674 | etot = -1077.76725730752
|
||||
30000 ekin = 142.135255524947 | erot = 110.165318126416 | epot = -1330.06783095566 | etot = -1077.7672573043
|
||||
31000 ekin = 142.945319498095 | erot = 109.26906345586 | epot = -1329.98164025322 | etot = -1077.76725729927
|
||||
32000 ekin = 143.550508334477 | erot = 108.646435343349 | epot = -1329.96420097205 | etot = -1077.76725729422
|
||||
33000 ekin = 143.94192379333 | erot = 108.385261854402 | epot = -1330.09444293819 | etot = -1077.76725729046
|
||||
34000 ekin = 144.112039801496 | erot = 108.556164698166 | epot = -1330.43546178798 | etot = -1077.76725728832
|
||||
35000 ekin = 144.054908300964 | erot = 109.203418763406 | epot = -1331.02558435228 | etot = -1077.76725728791
|
||||
36000 ekin = 143.757709793102 | erot = 110.342536293123 | epot = -1331.86750337561 | etot = -1077.76725728938
|
||||
37000 ekin = 143.224204313506 | erot = 111.95088434885 | epot = -1332.942345956 | etot = -1077.76725729365
|
||||
38000 ekin = 142.457513980673 | erot = 113.968727530034 | epot = -1334.19349881072 | etot = -1077.76725730001
|
||||
39000 ekin = 141.463565854942 | erot = 116.29723735485 | epot = -1335.52806051882 | etot = -1077.76725730903
|
||||
40000 ekin = 140.250124908962 | erot = 118.793122406283 | epot = -1336.81050463699 | etot = -1077.76725732174
|
||||
41000 ekin = 138.820773211814 | erot = 121.268568926308 | epot = -1337.85659947459 | etot = -1077.76725733647
|
||||
42000 ekin = 137.182796339923 | erot = 123.506485031842 | epot = -1338.45653872253 | etot = -1077.76725735076
|
||||
43000 ekin = 135.367500581476 | erot = 125.29033107441 | epot = -1338.42508901096 | etot = -1077.76725735508
|
||||
44000 ekin = 133.337269375167 | erot = 126.415468495777 | epot = -1337.51999529678 | etot = -1077.76725742584
|
||||
45000 ekin = 131.439049413892 | erot = 126.724836949372 | epot = -1335.93114371325 | etot = -1077.76725734999
|
||||
46000 ekin = 129.845441134595 | erot = 126.391857491267 | epot = -1334.00455608503 | etot = -1077.76725745917
|
||||
47000 ekin = 128.256459545521 | erot = 125.565939986762 | epot = -1331.58965689646 | etot = -1077.76725736418
|
||||
48000 ekin = 127.882214731217 | erot = 124.234254983921 | epot = -1329.88372728254 | etot = -1077.76725756741
|
||||
49000 ekin = 127.351717354214 | erot = 122.498251564086 | epot = -1327.61722629563 | etot = -1077.76725737733
|
||||
50000 ekin = 127.042187382637 | erot = 120.712825414822 | epot = -1325.52227015942 | etot = -1077.76725736196
|
||||
51000 ekin = 126.939090812203 | erot = 119.088171838498 | epot = -1323.7945200008 | etot = -1077.7672573501
|
||||
52000 ekin = 127.052758247807 | erot = 117.797033031223 | epot = -1322.61704861958 | etot = -1077.76725734055
|
||||
53000 ekin = 127.367330865571 | erot = 116.951027484839 | epot = -1322.08561579165 | etot = -1077.76725744124
|
||||
54000 ekin = 127.699598694243 | erot = 116.588954946935 | epot = -1322.05581098738 | etot = -1077.7672573462
|
||||
55000 ekin = 128.765472970124 | erot = 116.722527775949 | epot = -1323.25525818877 | etot = -1077.76725744269
|
||||
56000 ekin = 129.745971272492 | erot = 117.329047803033 | epot = -1324.84227644251 | etot = -1077.76725736699
|
||||
57000 ekin = 130.68679923891 | erot = 118.336149226794 | epot = -1326.79020584606 | etot = -1077.76725738035
|
||||
58000 ekin = 131.547485886187 | erot = 119.658488175854 | epot = -1328.97323145072 | etot = -1077.76725738868
|
||||
59000 ekin = 132.288746551762 | erot = 121.192124361468 | epot = -1331.2481283112 | etot = -1077.76725739797
|
||||
60000 ekin = 132.889658039575 | erot = 122.813399448196 | epot = -1333.47031489469 | etot = -1077.76725740691
|
||||
61000 ekin = 133.34147638721 | erot = 124.387402689362 | epot = -1335.49613649179 | etot = -1077.76725741522
|
||||
62000 ekin = 133.649114161524 | erot = 125.778714754977 | epot = -1337.19508633847 | etot = -1077.76725742197
|
||||
63000 ekin = 133.82819881192 | erot = 126.867080850077 | epot = -1338.46253708695 | etot = -1077.76725742496
|
||||
64000 ekin = 133.906684651824 | erot = 127.563040672905 | epot = -1339.23698275248 | etot = -1077.76725742775
|
||||
65000 ekin = 133.909388287634 | erot = 127.810288982225 | epot = -1339.48693469479 | etot = -1077.76725742493
|
||||
66000 ekin = 133.86081006735 | erot = 127.603400400037 | epot = -1339.23146788818 | etot = -1077.76725742079
|
||||
67000 ekin = 133.775485591323 | erot = 126.989915348575 | epot = -1338.53265835276 | etot = -1077.76725741286
|
||||
68000 ekin = 133.656407434476 | erot = 126.056031307506 | epot = -1337.47969615099 | etot = -1077.76725740901
|
||||
69000 ekin = 133.498245523806 | erot = 124.901121868324 | epot = -1336.16662479387 | etot = -1077.76725740175
|
||||
70000 ekin = 133.29399842671 | erot = 123.635623442427 | epot = -1334.69687926337 | etot = -1077.76725739423
|
||||
71000 ekin = 133.029392386924 | erot = 122.365171367186 | epot = -1333.16182114485 | etot = -1077.76725739074
|
||||
72000 ekin = 132.685056689193 | erot = 121.171597639892 | epot = -1331.62391171537 | etot = -1077.76725738628
|
||||
73000 ekin = 132.251376493387 | erot = 120.116099015078 | epot = -1330.13473289197 | etot = -1077.76725738351
|
||||
74000 ekin = 131.726574812548 | erot = 119.247057316129 | epot = -1328.74088951045 | etot = -1077.76725738177
|
||||
75000 ekin = 131.110698166934 | erot = 118.598252474103 | epot = -1327.47620801944 | etot = -1077.7672573784
|
||||
76000 ekin = 130.422389067205 | erot = 118.195180955537 | epot = -1326.38482739773 | etot = -1077.76725737499
|
||||
77000 ekin = 129.697453900293 | erot = 118.05495085627 | epot = -1325.51966212761 | etot = -1077.76725737104
|
||||
78000 ekin = 128.983808987508 | erot = 118.189138027539 | epot = -1324.94020438318 | etot = -1077.76725736813
|
||||
79000 ekin = 128.33503884882 | erot = 118.595476281743 | epot = -1324.69777249594 | etot = -1077.76725736537
|
||||
80000 ekin = 127.800117751073 | erot = 119.26689064397 | epot = -1324.83426576002 | etot = -1077.76725736498
|
||||
81000 ekin = 127.407996010304 | erot = 120.178391162382 | epot = -1325.35364454144 | etot = -1077.76725736875
|
||||
82000 ekin = 127.161473447285 | erot = 121.280514709077 | epot = -1326.20924553086 | etot = -1077.76725737449
|
||||
83000 ekin = 127.04595184901 | erot = 122.504106964497 | epot = -1327.31731619533 | etot = -1077.76725738182
|
||||
84000 ekin = 127.034443068044 | erot = 123.770035256801 | epot = -1328.57173571383 | etot = -1077.76725738899
|
||||
85000 ekin = 127.100009803031 | erot = 125.002871400657 | epot = -1329.87013859938 | etot = -1077.7672573957
|
||||
86000 ekin = 127.209916231691 | erot = 126.126063406782 | epot = -1331.10323704296 | etot = -1077.76725740449
|
||||
87000 ekin = 127.33974310822 | erot = 127.079810479666 | epot = -1332.186810994 | etot = -1077.76725740611
|
||||
88000 ekin = 127.492851572889 | erot = 127.842496747421 | epot = -1333.1026057236 | etot = -1077.76725740329
|
||||
89000 ekin = 127.697668813164 | erot = 128.428193060101 | epot = -1333.89311927022 | etot = -1077.76725739695
|
||||
90000 ekin = 128.002367682838 | erot = 128.890624121692 | epot = -1334.66024919208 | etot = -1077.76725738755
|
||||
91000 ekin = 128.464258986688 | erot = 129.314890049746 | epot = -1335.54640641371 | etot = -1077.76725737728
|
||||
92000 ekin = 129.138404881412 | erot = 129.795965407416 | epot = -1336.70162765837 | etot = -1077.76725736954
|
||||
93000 ekin = 130.05988004796 | erot = 130.410441748419 | epot = -1338.23757916353 | etot = -1077.76725736715
|
||||
94000 ekin = 131.22652253725 | erot = 131.190635069448 | epot = -1340.18441497914 | etot = -1077.76725737244
|
||||
95000 ekin = 132.586213223046 | erot = 132.107679404097 | epot = -1342.46115001118 | etot = -1077.76725738403
|
||||
96000 ekin = 134.044080427152 | erot = 133.075735506149 | epot = -1344.8870733339 | etot = -1077.7672574006
|
||||
97000 ekin = 135.476028603552 | erot = 133.967715320791 | epot = -1347.21100134248 | etot = -1077.76725741814
|
||||
98000 ekin = 136.748227204441 | erot = 134.641388466874 | epot = -1349.15687309791 | etot = -1077.76725742659
|
||||
99000 ekin = 137.752624159367 | erot = 134.99210077777 | epot = -1350.51198237554 | etot = -1077.7672574384
|
||||
100000 ekin = 138.392477025647 | erot = 134.944608034508 | epot = -1351.10434250636 | etot = -1077.76725744621
|
||||
100000 315.83543 -1390.6819 39.577599 -1212.7119 -0.012722464 6.1629505e+08
|
||||
Loop time of 85.2132 on 1 procs for 100000 steps with 148 atoms
|
||||
|
||||
Performance: 1.730 ns/day, 13.875 hours/ns, 1173.528 timesteps/s, 173.682 katom-step/s
|
||||
99.8% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 81.71 | 81.71 | 81.71 | 0.0 | 95.89
|
||||
Bond | 1.103 | 1.103 | 1.103 | 0.0 | 1.29
|
||||
Neigh | 0.017589 | 0.017589 | 0.017589 | 0.0 | 0.02
|
||||
Comm | 0.055508 | 0.055508 | 0.055508 | 0.0 | 0.07
|
||||
Output | 0.1581 | 0.1581 | 0.1581 | 0.0 | 0.19
|
||||
Modify | 2.0369 | 2.0369 | 2.0369 | 0.0 | 2.39
|
||||
Other | | 0.132 | | | 0.15
|
||||
|
||||
Nlocal: 148 ave 148 max 148 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 4199 ave 4199 max 4199 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 4199
|
||||
Ave neighs/atom = 28.371622
|
||||
Ave special neighs/atom = 6
|
||||
Neighbor list builds = 100
|
||||
Dangerous builds = 0
|
||||
|
||||
write_data last_config.${number}.* nocoeff
|
||||
write_data last_config.5.* nocoeff
|
||||
System init for write_data ...
|
||||
Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule
|
||||
#write_restart last_config.${number}.*
|
||||
Total wall time: 0:01:25
|
||||
@ -0,0 +1,286 @@
|
||||
LAMMPS (17 Apr 2024 - Development - patch_17Apr2024-174-g749e259294-modified)
|
||||
# LAMMPS input file in real units via oxdna lj2real.py, date 2024-05-19
|
||||
variable number equal 5
|
||||
variable ofreq equal 1000
|
||||
variable efreq equal 1000
|
||||
variable T equal 300.0
|
||||
variable rhos equal 0.2
|
||||
|
||||
units real
|
||||
|
||||
dimension 3
|
||||
|
||||
newton on
|
||||
|
||||
boundary p p p
|
||||
|
||||
atom_style hybrid bond ellipsoid oxdna
|
||||
WARNING: Atom style hybrid defines both, per-type and per-atom masses; both must be set, but only per-atom masses will be used (../atom_vec_hybrid.cpp:132)
|
||||
atom_modify sort 0 8.518
|
||||
|
||||
# Pair interactions require lists of neighbours to be calculated
|
||||
neighbor 17.036 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
read_data data.dsring
|
||||
Reading data file ...
|
||||
orthogonal box = (0 0 0) to (851 851 851)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
148 atoms
|
||||
reading velocities ...
|
||||
148 velocities
|
||||
scanning bonds ...
|
||||
1 = max bonds/atom
|
||||
148 ellipsoids
|
||||
orthogonal box = (0 0 0) to (851 851 851)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading bonds ...
|
||||
148 bonds
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 0 0
|
||||
special bond factors coul: 0 0 0
|
||||
2 = max # of 1-2 neighbors
|
||||
2 = max # of 1-3 neighbors
|
||||
4 = max # of 1-4 neighbors
|
||||
6 = max # of special neighbors
|
||||
special bonds CPU = 0.001 seconds
|
||||
read_data CPU = 0.015 seconds
|
||||
|
||||
set atom * mass 315.8376
|
||||
Setting atom values ...
|
||||
148 settings made for mass
|
||||
|
||||
group all type 1 4
|
||||
148 atoms in group all
|
||||
|
||||
# oxDNA2 bond interactions - FENE backbone
|
||||
bond_style oxdna2/fene
|
||||
bond_coeff * 11.92337812042065 2.1295 6.4430152
|
||||
special_bonds lj 0 1 1
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 1 1
|
||||
special bond factors coul: 0 0 0
|
||||
2 = max # of 1-2 neighbors
|
||||
2 = max # of 1-3 neighbors
|
||||
4 = max # of 1-4 neighbors
|
||||
6 = max # of special neighbors
|
||||
special bonds CPU = 0.000 seconds
|
||||
|
||||
# oxDNA2 pair interactions
|
||||
pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
|
||||
pair_coeff * * oxdna2/excv 11.92337812042065 5.9626 5.74965 11.92337812042065 4.38677 4.259 11.92337812042065 2.81094 2.72576
|
||||
pair_coeff * * oxdna2/stk seqdep ${T} 8.06199211612242 0.005309213 0.70439070204273 3.4072 7.6662 2.72576 6.3885 1.3 0.0 0.8 0.9 0.0 0.95 0.9 0.0 0.95 2.0 0.65 2.0 0.65
|
||||
pair_coeff * * oxdna2/stk seqdep 300 8.06199211612242 0.005309213 0.70439070204273 3.4072 7.6662 2.72576 6.3885 1.3 0.0 0.8 0.9 0.0 0.95 0.9 0.0 0.95 2.0 0.65 2.0 0.65
|
||||
pair_coeff * * oxdna2/hbond seqdep 0.0 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0.0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45
|
||||
pair_coeff 1 4 oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45
|
||||
pair_coeff 2 3 oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45
|
||||
pair_coeff * * oxdna2/xstk 3.9029021145006 4.89785 5.74965 4.21641 5.57929 2.25 0.791592654 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
|
||||
pair_coeff * * oxdna2/coaxstk 4.80673207785863 3.4072 5.1108 1.87396 4.94044 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793
|
||||
pair_coeff * * oxdna2/dh ${T} ${rhos} 0.815
|
||||
pair_coeff * * oxdna2/dh 300 ${rhos} 0.815
|
||||
pair_coeff * * oxdna2/dh 300 0.2 0.815
|
||||
|
||||
# NVE ensemble
|
||||
fix 1 all nve/asphere
|
||||
#fix 2 all langevin ${T} ${T} 4265.0 457145 angmom 10
|
||||
|
||||
timestep 0.01706
|
||||
|
||||
#comm_style tiled
|
||||
fix 3 all balance 1000 1.03 shift xyz 10 1.03
|
||||
comm_modify cutoff 32.4
|
||||
|
||||
compute quat all property/atom quatw quati quatj quatk
|
||||
|
||||
compute erot all erotate/asphere
|
||||
compute ekin all ke
|
||||
compute epot all pe
|
||||
variable erot equal c_erot
|
||||
variable ekin equal c_ekin
|
||||
variable epot equal c_epot
|
||||
variable etot equal c_erot+c_ekin+c_epot
|
||||
fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
|
||||
fix 5 all print 1000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
|
||||
|
||||
dump out all custom ${ofreq} out.${number}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz
|
||||
dump out all custom 1000 out.${number}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz
|
||||
dump out all custom 1000 out.5.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz
|
||||
dump_modify out sort id
|
||||
dump_modify out format line "%d %d %d %22.15le %22.15le %22.15le %d %d %d %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le"
|
||||
|
||||
run 100000
|
||||
Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 0 steps, check = yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 48.032697
|
||||
ghost atom cutoff = 48.032697
|
||||
binsize = 24.016348, bins = 36 36 36
|
||||
5 neighbor lists, perpetual/occasional/extra = 5 0 0
|
||||
(1) pair oxdna2/excv, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
(2) pair oxdna2/hbond, perpetual, copy from (1)
|
||||
attributes: half, newton on
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(3) pair oxdna2/xstk, perpetual, copy from (1)
|
||||
attributes: half, newton on
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(4) pair oxdna2/coaxstk, perpetual, copy from (1)
|
||||
attributes: half, newton on
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(5) pair oxdna2/dh, perpetual, copy from (1)
|
||||
attributes: half, newton on
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
WARNING: Communication cutoff adjusted to 48.03269686950012 (../comm.cpp:739)
|
||||
0 ekin = 122.015812851425 | erot = 125.402528675609 | epot = -1325.18559882055 | etot = -1077.76725729351
|
||||
Per MPI rank memory allocation (min/avg/max) = 7.619 | 7.668 | 7.742 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press Volume
|
||||
0 278.46107 -1367.7166 42.531022 -1203.1698 -0.0059756093 6.1629505e+08
|
||||
1000 ekin = 122.370905858635 | erot = 126.447129514011 | epot = -1326.58529267981 | etot = -1077.76725730716
|
||||
2000 ekin = 122.691275133791 | erot = 127.497291822808 | epot = -1327.95582427469 | etot = -1077.76725731809
|
||||
3000 ekin = 122.920677842253 | erot = 128.459039892254 | epot = -1329.14697506148 | etot = -1077.76725732698
|
||||
4000 ekin = 123.015104309575 | erot = 129.250631266888 | epot = -1330.03299290867 | etot = -1077.7672573322
|
||||
5000 ekin = 122.957006098101 | erot = 129.822304188925 | epot = -1330.54656761964 | etot = -1077.76725733262
|
||||
6000 ekin = 122.758396503728 | erot = 130.158463496346 | epot = -1330.68411732949 | etot = -1077.76725732941
|
||||
7000 ekin = 122.444997038108 | erot = 130.272135143499 | epot = -1330.48438950495 | etot = -1077.76725732334
|
||||
8000 ekin = 122.055455926323 | erot = 130.202756105441 | epot = -1330.02546934809 | etot = -1077.76725731633
|
||||
9000 ekin = 121.639778047767 | erot = 130.001921534637 | epot = -1329.40895689073 | etot = -1077.76725730833
|
||||
10000 ekin = 121.255561480543 | erot = 129.724613334694 | epot = -1328.74743211587 | etot = -1077.76725730063
|
||||
11000 ekin = 120.959150047793 | erot = 129.417382591737 | epot = -1328.14378993382 | etot = -1077.76725729429
|
||||
12000 ekin = 120.804873255897 | erot = 129.110119861453 | epot = -1327.68225040707 | etot = -1077.76725728972
|
||||
13000 ekin = 120.846923120261 | erot = 128.8114527819 | epot = -1327.42563318933 | etot = -1077.76725728717
|
||||
14000 ekin = 121.124227416955 | erot = 128.51031885751 | epot = -1327.40180356072 | etot = -1077.76725728625
|
||||
15000 ekin = 121.666723735015 | erot = 128.179805529184 | epot = -1327.61378655278 | etot = -1077.76725728858
|
||||
16000 ekin = 122.48420413773 | erot = 127.771410123803 | epot = -1328.02287155596 | etot = -1077.76725729443
|
||||
17000 ekin = 123.554901437623 | erot = 127.223257664152 | epot = -1328.54541640317 | etot = -1077.76725730139
|
||||
18000 ekin = 124.838358543238 | erot = 126.479155255366 | epot = -1329.0847711071 | etot = -1077.7672573085
|
||||
19000 ekin = 126.271030938727 | erot = 125.497490625601 | epot = -1329.53577887969 | etot = -1077.76725731536
|
||||
20000 ekin = 127.785246119996 | erot = 124.269691231029 | epot = -1329.82219466646 | etot = -1077.76725731543
|
||||
21000 ekin = 129.341920134184 | erot = 122.835059904169 | epot = -1329.94423735083 | etot = -1077.76725731247
|
||||
22000 ekin = 130.91969100621 | erot = 121.2628767273 | epot = -1329.94982504098 | etot = -1077.76725730747
|
||||
23000 ekin = 132.506705548099 | erot = 119.637982005259 | epot = -1329.91194485557 | etot = -1077.76725730222
|
||||
24000 ekin = 134.092490326558 | erot = 118.039019184419 | epot = -1329.89876681119 | etot = -1077.76725730022
|
||||
25000 ekin = 135.660464836621 | erot = 116.515685186213 | epot = -1329.94340732286 | etot = -1077.76725730003
|
||||
26000 ekin = 137.186778726603 | erot = 115.085213344396 | epot = -1330.03924937554 | etot = -1077.76725730454
|
||||
27000 ekin = 138.631216641226 | erot = 113.733576310578 | epot = -1330.13205025948 | etot = -1077.76725730767
|
||||
28000 ekin = 139.956351860934 | erot = 112.450817889845 | epot = -1330.17442705975 | etot = -1077.76725730897
|
||||
29000 ekin = 141.132095730946 | erot = 111.248013058276 | epot = -1330.14736609673 | etot = -1077.76725730751
|
||||
30000 ekin = 142.135255524949 | erot = 110.165318126416 | epot = -1330.06783095566 | etot = -1077.76725730429
|
||||
31000 ekin = 142.945319498097 | erot = 109.269063455861 | epot = -1329.98164025322 | etot = -1077.76725729926
|
||||
32000 ekin = 143.550508334479 | erot = 108.64643534335 | epot = -1329.96420097205 | etot = -1077.76725729422
|
||||
33000 ekin = 143.941923793332 | erot = 108.385261854403 | epot = -1330.09444293819 | etot = -1077.76725729046
|
||||
34000 ekin = 144.112039801499 | erot = 108.556164698166 | epot = -1330.43546178798 | etot = -1077.76725728831
|
||||
35000 ekin = 144.054908300967 | erot = 109.203418763407 | epot = -1331.02558435228 | etot = -1077.76725728791
|
||||
36000 ekin = 143.757709793105 | erot = 110.342536293123 | epot = -1331.8675033756 | etot = -1077.76725728938
|
||||
37000 ekin = 143.224204313509 | erot = 111.950884348849 | epot = -1332.942345956 | etot = -1077.76725729364
|
||||
38000 ekin = 142.457513980675 | erot = 113.968727530033 | epot = -1334.19349881072 | etot = -1077.76725730001
|
||||
39000 ekin = 141.463565854944 | erot = 116.297237354849 | epot = -1335.52806051882 | etot = -1077.76725730903
|
||||
40000 ekin = 140.250124908963 | erot = 118.793122406281 | epot = -1336.81050463698 | etot = -1077.76725732174
|
||||
41000 ekin = 138.820773211815 | erot = 121.268568926305 | epot = -1337.85659947459 | etot = -1077.76725733647
|
||||
42000 ekin = 137.182796339923 | erot = 123.506485031839 | epot = -1338.45653872252 | etot = -1077.76725735076
|
||||
43000 ekin = 135.367500581475 | erot = 125.290331074407 | epot = -1338.42508901096 | etot = -1077.76725735507
|
||||
44000 ekin = 133.337269375166 | erot = 126.415468495773 | epot = -1337.51999529677 | etot = -1077.76725742583
|
||||
45000 ekin = 131.43904941389 | erot = 126.724836949369 | epot = -1335.93114371325 | etot = -1077.76725734999
|
||||
46000 ekin = 129.845441134593 | erot = 126.391857491264 | epot = -1334.00455608502 | etot = -1077.76725745916
|
||||
47000 ekin = 128.256459545521 | erot = 125.565939986761 | epot = -1331.58965689646 | etot = -1077.76725736417
|
||||
48000 ekin = 127.882214731216 | erot = 124.23425498392 | epot = -1329.88372728254 | etot = -1077.7672575674
|
||||
49000 ekin = 127.351717354214 | erot = 122.498251564087 | epot = -1327.61722629563 | etot = -1077.76725737733
|
||||
50000 ekin = 127.042187382636 | erot = 120.712825414824 | epot = -1325.52227015942 | etot = -1077.76725736196
|
||||
51000 ekin = 126.939090812203 | erot = 119.088171838501 | epot = -1323.7945200008 | etot = -1077.76725735009
|
||||
52000 ekin = 127.052758247806 | erot = 117.797033031227 | epot = -1322.61704861958 | etot = -1077.76725734055
|
||||
53000 ekin = 127.36733086557 | erot = 116.951027484844 | epot = -1322.08561579166 | etot = -1077.76725744124
|
||||
54000 ekin = 127.699598694242 | erot = 116.588954946942 | epot = -1322.05581098738 | etot = -1077.7672573462
|
||||
55000 ekin = 128.765472970119 | erot = 116.722527775956 | epot = -1323.25525818877 | etot = -1077.76725744269
|
||||
56000 ekin = 129.745971272485 | erot = 117.329047803041 | epot = -1324.84227644252 | etot = -1077.76725736699
|
||||
57000 ekin = 130.686799238902 | erot = 118.336149226803 | epot = -1326.79020584605 | etot = -1077.76725738035
|
||||
58000 ekin = 131.547485886178 | erot = 119.658488175863 | epot = -1328.97323145072 | etot = -1077.76725738868
|
||||
59000 ekin = 132.288746551752 | erot = 121.192124361476 | epot = -1331.24812831119 | etot = -1077.76725739797
|
||||
60000 ekin = 132.889658039566 | erot = 122.813399448204 | epot = -1333.47031489469 | etot = -1077.76725740692
|
||||
61000 ekin = 133.341476387201 | erot = 124.387402689369 | epot = -1335.49613649179 | etot = -1077.76725741522
|
||||
62000 ekin = 133.649114161516 | erot = 125.778714754983 | epot = -1337.19508633847 | etot = -1077.76725742197
|
||||
63000 ekin = 133.828198811913 | erot = 126.867080850083 | epot = -1338.46253708696 | etot = -1077.76725742496
|
||||
64000 ekin = 133.906684651817 | erot = 127.56304067291 | epot = -1339.23698275248 | etot = -1077.76725742776
|
||||
65000 ekin = 133.909388287628 | erot = 127.81028898223 | epot = -1339.48693469479 | etot = -1077.76725742493
|
||||
66000 ekin = 133.860810067346 | erot = 127.603400400042 | epot = -1339.23146788819 | etot = -1077.7672574208
|
||||
67000 ekin = 133.775485591319 | erot = 126.98991534858 | epot = -1338.53265835276 | etot = -1077.76725741286
|
||||
68000 ekin = 133.656407434473 | erot = 126.056031307511 | epot = -1337.479696151 | etot = -1077.76725740901
|
||||
69000 ekin = 133.498245523803 | erot = 124.901121868328 | epot = -1336.16662479388 | etot = -1077.76725740175
|
||||
70000 ekin = 133.293998426708 | erot = 123.635623442431 | epot = -1334.69687926337 | etot = -1077.76725739423
|
||||
71000 ekin = 133.029392386922 | erot = 122.36517136719 | epot = -1333.16182114486 | etot = -1077.76725739074
|
||||
72000 ekin = 132.685056689192 | erot = 121.171597639896 | epot = -1331.62391171537 | etot = -1077.76725738628
|
||||
73000 ekin = 132.251376493386 | erot = 120.116099015081 | epot = -1330.13473289197 | etot = -1077.76725738351
|
||||
74000 ekin = 131.726574812547 | erot = 119.247057316132 | epot = -1328.74088951045 | etot = -1077.76725738177
|
||||
75000 ekin = 131.110698166933 | erot = 118.598252474106 | epot = -1327.47620801944 | etot = -1077.7672573784
|
||||
76000 ekin = 130.422389067204 | erot = 118.195180955539 | epot = -1326.38482739773 | etot = -1077.76725737499
|
||||
77000 ekin = 129.697453900292 | erot = 118.054950856271 | epot = -1325.51966212761 | etot = -1077.76725737104
|
||||
78000 ekin = 128.983808987507 | erot = 118.18913802754 | epot = -1324.94020438318 | etot = -1077.76725736813
|
||||
79000 ekin = 128.33503884882 | erot = 118.595476281743 | epot = -1324.69777249594 | etot = -1077.76725736537
|
||||
80000 ekin = 127.800117751073 | erot = 119.266890643969 | epot = -1324.83426576002 | etot = -1077.76725736498
|
||||
81000 ekin = 127.407996010304 | erot = 120.178391162381 | epot = -1325.35364454144 | etot = -1077.76725736875
|
||||
82000 ekin = 127.161473447286 | erot = 121.280514709075 | epot = -1326.20924553085 | etot = -1077.76725737449
|
||||
83000 ekin = 127.045951849011 | erot = 122.504106964495 | epot = -1327.31731619533 | etot = -1077.76725738182
|
||||
84000 ekin = 127.034443068046 | erot = 123.770035256799 | epot = -1328.57173571383 | etot = -1077.76725738899
|
||||
85000 ekin = 127.100009803033 | erot = 125.002871400656 | epot = -1329.87013859939 | etot = -1077.7672573957
|
||||
86000 ekin = 127.209916231694 | erot = 126.12606340678 | epot = -1331.10323704296 | etot = -1077.76725740449
|
||||
87000 ekin = 127.339743108223 | erot = 127.079810479664 | epot = -1332.186810994 | etot = -1077.76725740611
|
||||
88000 ekin = 127.492851572892 | erot = 127.842496747418 | epot = -1333.1026057236 | etot = -1077.76725740329
|
||||
89000 ekin = 127.697668813166 | erot = 128.428193060097 | epot = -1333.89311927021 | etot = -1077.76725739695
|
||||
90000 ekin = 128.00236768284 | erot = 128.890624121688 | epot = -1334.66024919208 | etot = -1077.76725738755
|
||||
91000 ekin = 128.464258986691 | erot = 129.314890049742 | epot = -1335.54640641371 | etot = -1077.76725737728
|
||||
92000 ekin = 129.138404881414 | erot = 129.795965407411 | epot = -1336.70162765836 | etot = -1077.76725736954
|
||||
93000 ekin = 130.059880047962 | erot = 130.410441748414 | epot = -1338.23757916353 | etot = -1077.76725736715
|
||||
94000 ekin = 131.226522537251 | erot = 131.190635069444 | epot = -1340.18441497913 | etot = -1077.76725737244
|
||||
95000 ekin = 132.586213223046 | erot = 132.107679404094 | epot = -1342.46115001117 | etot = -1077.76725738403
|
||||
96000 ekin = 134.044080427153 | erot = 133.075735506146 | epot = -1344.88707333389 | etot = -1077.76725740059
|
||||
97000 ekin = 135.476028603552 | erot = 133.967715320788 | epot = -1347.21100134248 | etot = -1077.76725741814
|
||||
98000 ekin = 136.748227204441 | erot = 134.641388466873 | epot = -1349.15687309791 | etot = -1077.76725742659
|
||||
99000 ekin = 137.752624159367 | erot = 134.99210077777 | epot = -1350.51198237554 | etot = -1077.7672574384
|
||||
100000 ekin = 138.392477025646 | erot = 134.94460803451 | epot = -1351.10434250636 | etot = -1077.76725744621
|
||||
100000 315.83543 -1390.6819 39.577599 -1212.7119 -0.012722464 6.1629505e+08
|
||||
Loop time of 30.2255 on 4 procs for 100000 steps with 148 atoms
|
||||
|
||||
Performance: 4.877 ns/day, 4.921 hours/ns, 3308.461 timesteps/s, 489.652 katom-step/s
|
||||
99.6% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 16.766 | 22.691 | 26.962 | 89.3 | 75.07
|
||||
Bond | 0.28821 | 0.30757 | 0.32075 | 2.3 | 1.02
|
||||
Neigh | 0.008451 | 0.008527 | 0.008607 | 0.1 | 0.03
|
||||
Comm | 2.0101 | 6.3007 | 12.277 | 170.6 | 20.85
|
||||
Output | 0.051655 | 0.054646 | 0.056776 | 0.9 | 0.18
|
||||
Modify | 0.53953 | 0.56983 | 0.63795 | 5.3 | 1.89
|
||||
Other | | 0.2934 | | | 0.97
|
||||
|
||||
Nlocal: 37 ave 38 max 36 min
|
||||
Histogram: 1 0 0 0 0 2 0 0 0 1
|
||||
Nghost: 111 ave 112 max 110 min
|
||||
Histogram: 1 0 0 0 0 2 0 0 0 1
|
||||
Neighs: 1049.75 ave 1288 max 753 min
|
||||
Histogram: 1 0 0 1 0 0 0 0 0 2
|
||||
|
||||
Total # of neighbors = 4199
|
||||
Ave neighs/atom = 28.371622
|
||||
Ave special neighs/atom = 6
|
||||
Neighbor list builds = 100
|
||||
Dangerous builds = 0
|
||||
|
||||
write_data last_config.${number}.* nocoeff
|
||||
write_data last_config.5.* nocoeff
|
||||
System init for write_data ...
|
||||
Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule
|
||||
#write_restart last_config.${number}.*
|
||||
Total wall time: 0:00:30
|
||||
@ -0,0 +1,68 @@
|
||||
LAMMPS data file in real units via oxdna lj2real.py, date 2024-05-19
|
||||
|
||||
10 atoms
|
||||
4 atom types
|
||||
8 bonds
|
||||
1 bond types
|
||||
10 ellipsoids
|
||||
|
||||
-170 170 xlo xhi
|
||||
-170 170 ylo yhi
|
||||
-170 170 zlo zhi
|
||||
|
||||
Masses
|
||||
|
||||
1 315.8376
|
||||
2 315.8376
|
||||
3 315.8376
|
||||
4 315.8376
|
||||
|
||||
Atoms # hybrid
|
||||
|
||||
1 1 -2.8740969069282687 -3.723118600434732 5.494693518792015 1 1 1.0016462505133576 0 0 0
|
||||
2 2 -2.7379071878387986 -6.079929519421481 10.066032484018534 1 1 1.0016462505133576 0 0 0
|
||||
3 3 -1.110437385073819 -7.791537941948432 13.848676172779387 1 1 1.0016462505133576 0 0 0
|
||||
4 4 1.4306089998272526 -8.354886654263622 17.79828313773629 1 1 1.0016462505133576 0 0 0
|
||||
5 1 3.9498326729322186 -6.646891787969407 20.657842369456382 1 1 1.0016462505133576 0 0 0
|
||||
6 4 -3.801540967989063 0.7719150486872158 21.01300417274477 2 1 1.0016462505133576 0 0 0
|
||||
7 1 -0.287657468030243 1.787063409177335 17.702181979507532 2 1 1.0016462505133576 0 0 0
|
||||
8 2 2.8086617684512323 1.5040732709582532 14.656350509768911 2 1 1.0016462505133576 0 0 0
|
||||
9 3 5.165059071666839 0.3988634556159852 10.50699529001116 2 1 1.0016462505133576 0 0 0
|
||||
10 4 6.817789789050184 -3.1038996716078557 8.419212766646357 2 1 1.0016462505133576 0 0 0
|
||||
|
||||
Velocities
|
||||
|
||||
1 0.0015993537866009029 -0.000680681865016988 -0.00014678467473993874 1.3034875452014287 -0.6725260292370423 1.5263182328899618
|
||||
2 0.0008422431968202534 -0.0002471920411024751 0.0007894382186365997 -0.32615096872390803 -0.0034351199136194157 -0.9136220137417161
|
||||
3 -0.0011446153381118452 0.00041850425643063176 -0.00045926941555484915 1.7184317758530245 2.6050996986101502 -0.47065934236730145
|
||||
4 -0.0011077496385743138 0.0002472924939324634 -0.00034633314311123244 -0.5778245520276679 1.752085001878762 -0.24048635097513535
|
||||
5 0.0004072478403200556 -0.0012804934445473403 0.0008610591638760516 0.23142339993018143 0.3972766524238825 1.363641236078021
|
||||
6 0.00017968178785700138 -0.00024308968845109275 0.00014280408309295725 0.1704955558294103 -1.3525913126172677 1.5501424653239764
|
||||
7 -4.108556803115003e-05 0.00023724044475488887 -0.00013843701960263193 0.7809156374181498 -2.1218743676572576 0.2975087875146955
|
||||
8 -0.00035835254321313353 0.0008579277312926632 0.0019500603503724006 -0.711656157643413 -2.0351916264105014 -0.7613827970610736
|
||||
9 -0.0008730894357027041 -0.00039026927657647716 0.0002796967510539106 -1.193834703375802 1.023301140813147 -1.8342354268493246
|
||||
10 0.0009421885758929626 -0.0005326396944231774 0.0006296458639527654 -0.24420734152643714 1.5633648178267814 0.6376075187926279
|
||||
|
||||
Bonds
|
||||
|
||||
1 1 1 2
|
||||
2 1 2 3
|
||||
3 1 3 4
|
||||
4 1 4 5
|
||||
5 1 6 7
|
||||
6 1 7 8
|
||||
7 1 8 9
|
||||
8 1 9 10
|
||||
|
||||
Ellipsoids
|
||||
|
||||
1 9.999999997766462 9.999999997766462 9.999999997766462 0.9890278201757743 0.01779228232037064 -0.14337734159225404 0.030827642240801516
|
||||
2 9.999999997766462 9.999999997766462 9.999999997766462 0.939687458852748 0.04174166924055095 -0.023337773785056866 0.338674565089608
|
||||
3 9.999999997766462 9.999999997766462 9.999999997766462 0.8210113150655425 0.03012140921736572 0.017666019956944813 0.5698429897612057
|
||||
4 9.999999997766462 9.999999997766462 9.999999997766462 0.6623662858285051 -0.028186343967346823 0.022942552517501488 0.7482981175276918
|
||||
5 9.999999997766462 9.999999997766462 9.999999997766462 0.3601488726765216 0.0513614985821682 0.0724224158335286 0.9286602067807472
|
||||
6 9.999999997766462 9.999999997766462 9.999999997766462 0.11941234710084649 0.9244660117493703 -0.35317942248051865 -0.07979711784524246
|
||||
7 9.999999997766462 9.999999997766462 9.999999997766462 -0.17949125421205164 0.7412884899431119 -0.6379094464220707 0.1065166771202199
|
||||
8 9.999999997766462 9.999999997766462 9.999999997766462 -0.10483691088405202 0.5508895999584645 -0.8250090480220789 0.06992811634525403
|
||||
9 9.999999997766462 9.999999997766462 9.999999997766462 0.07777239911646 -0.3724087549185288 0.9103052384821374 -0.1631181963720798
|
||||
10 9.999999997766462 9.999999997766462 9.999999997766462 0.16279109707978262 0.027148630125149613 0.9849325709665359 -0.0516705065113425
|
||||
@ -0,0 +1,73 @@
|
||||
# LAMMPS input file in real units via oxdna lj2real.py, date 2024-05-19
|
||||
variable number equal 1
|
||||
variable ofreq equal 1000
|
||||
variable efreq equal 1000
|
||||
variable T equal 300.0
|
||||
variable rhos equal 0.2
|
||||
|
||||
units real
|
||||
|
||||
dimension 3
|
||||
|
||||
newton on
|
||||
|
||||
boundary p p p
|
||||
|
||||
atom_style hybrid bond ellipsoid oxdna
|
||||
atom_modify sort 0 8.518
|
||||
|
||||
# Pair interactions require lists of neighbours to be calculated
|
||||
neighbor 17.036 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
read_data data.duplex1
|
||||
|
||||
set atom * mass 315.8376
|
||||
|
||||
group all type 1 4
|
||||
|
||||
# oxDNA2 bond interactions - FENE backbone
|
||||
bond_style oxdna2/fene
|
||||
bond_coeff * 11.92337812042065 2.1295 6.4430152
|
||||
special_bonds lj 0 1 1
|
||||
|
||||
# oxDNA2 pair interactions
|
||||
pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
|
||||
pair_coeff * * oxdna2/excv 11.92337812042065 5.9626 5.74965 11.92337812042065 4.38677 4.259 11.92337812042065 2.81094 2.72576
|
||||
pair_coeff * * oxdna2/stk seqav ${T} 8.06199211612242 0.005309213 0.70439070204273 3.4072 7.6662 2.72576 6.3885 1.3 0.0 0.8 0.9 0.0 0.95 0.9 0.0 0.95 2.0 0.65 2.0 0.65
|
||||
pair_coeff * * oxdna2/hbond seqav 0.0 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0.0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45
|
||||
pair_coeff 1 4 oxdna2/hbond seqav 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45
|
||||
pair_coeff 2 3 oxdna2/hbond seqav 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45
|
||||
pair_coeff * * oxdna2/xstk 3.9029021145006 4.89785 5.74965 4.21641 5.57929 2.25 0.791592654 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
|
||||
pair_coeff * * oxdna2/coaxstk 4.80673207785863 3.4072 5.1108 1.87396 4.94044 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793
|
||||
pair_coeff * * oxdna2/dh ${T} ${rhos} 0.815
|
||||
|
||||
# NVE ensemble
|
||||
fix 1 all nve/asphere
|
||||
#fix 2 all langevin ${T} ${T} 4265.0 457145 angmom 10
|
||||
|
||||
timestep 0.01706
|
||||
|
||||
#comm_style tiled
|
||||
fix 3 all balance 1000 1.03 shift xyz 10 1.03
|
||||
comm_modify cutoff 32.4
|
||||
|
||||
compute quat all property/atom quatw quati quatj quatk
|
||||
|
||||
compute erot all erotate/asphere
|
||||
compute ekin all ke
|
||||
compute epot all pe
|
||||
variable erot equal c_erot
|
||||
variable ekin equal c_ekin
|
||||
variable epot equal c_epot
|
||||
variable etot equal c_erot+c_ekin+c_epot
|
||||
fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
|
||||
|
||||
dump out all custom ${ofreq} out.${number}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz
|
||||
dump_modify out sort id
|
||||
dump_modify out format line "%d %d %d %22.15le %22.15le %22.15le %d %d %d %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le"
|
||||
|
||||
run 1000000
|
||||
|
||||
write_data last_config.${number}.* nocoeff
|
||||
#write_restart last_config.${number}.*
|
||||
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
@ -0,0 +1,91 @@
|
||||
LAMMPS data file in real units via oxdna lj2real.py, date 2024-05-19
|
||||
|
||||
16 atoms
|
||||
4 atom types
|
||||
13 bonds
|
||||
1 bond types
|
||||
16 ellipsoids
|
||||
|
||||
-170 170 xlo xhi
|
||||
-170 170 ylo yhi
|
||||
-170 170 zlo zhi
|
||||
|
||||
Masses
|
||||
|
||||
1 315.8376
|
||||
2 315.8376
|
||||
3 315.8376
|
||||
4 315.8376
|
||||
|
||||
Atoms # hybrid
|
||||
|
||||
1 1 -5.224492277936935 -5.6003990662830665 3.072035980595378 1 1 1.0016462505133576 0 0 0
|
||||
2 2 -3.855482258589815 -8.54410812515585 6.182955020430966 1 1 1.0016462505133576 0 0 0
|
||||
3 3 -0.8418698080395857 -10.56041032511679 9.10967975032824 1 1 1.0016462505133576 0 0 0
|
||||
4 4 2.502394065492512 -10.715431837829685 12.145744722571814 1 1 1.0016462505133576 0 0 0
|
||||
5 1 5.355178690564601 -8.674171903962998 15.067785212133312 1 1 1.0016462505133576 0 0 0
|
||||
6 2 6.7305169669220595 -5.763569949980494 18.347908888941284 1 1 1.0016462505133576 0 0 0
|
||||
7 3 6.061219006086631 -3.4238594469157198 21.88758604427721 1 1 1.0016462505133576 0 0 0
|
||||
8 4 4.001186577913306 -2.576839632838177 26.12300846270287 1 1 1.0016462505133576 0 0 0
|
||||
9 1 3.454997351061381 -12.298079702286948 26.05718083554597 2 1 1.0016462505133576 0 0 0
|
||||
10 2 -0.2728181587270111 -11.028698363238112 23.169872406755868 2 1 1.0016462505133576 0 0 0
|
||||
11 3 -2.692868178466912 -7.73787195036868 20.549852065183913 2 1 1.0016462505133576 0 0 0
|
||||
12 4 -3.316857346830113 -4.145374554885233 17.08862230448963 2 1 1.0016462505133576 0 0 0
|
||||
13 1 -0.5308965342198838 -0.6095451431748122 13.28229291571604 3 1 1.0016462505133576 0 0 0
|
||||
14 2 1.5233668194980015 -0.46991432454420656 8.699204689407908 3 1 1.0016462505133576 0 0 0
|
||||
15 3 3.844548159551531 -2.026909836907328 5.074452450044903 3 1 1.0016462505133576 0 0 0
|
||||
16 4 4.325141724684425 -4.740799489595668 1.4104749932020408 3 1 1.0016462505133576 0 0 0
|
||||
|
||||
Velocities
|
||||
|
||||
1 0.00026896558742537556 0.00011298695236274073 0.001242364337461123 0.7538466533118467 -1.2587520584415195 -1.1163576881067447
|
||||
2 -0.00019946914535880285 0.0013465785184092233 -0.0009479872206420321 -0.13024003640483983 -0.5006975787807386 0.17048535791572514
|
||||
3 -0.0010377647810347322 -0.0006804774738725614 -0.000302697462953215 -0.15638545864527348 -0.2683843524758034 -0.6295604792026762
|
||||
4 -0.0011968051721949484 -0.002808404437492725 0.00016214368951061121 -0.7029471277015998 1.2169631204234201 1.42700472482703
|
||||
5 -0.0008046113463391788 -0.001142874812754601 -0.0006767129075723855 0.304218367349499 -0.4005571162913614 0.5710347488390389
|
||||
6 -0.00023475461149269044 0.000959484075931813 0.0007283860029089665 0.3921776444343422 -2.399417440979843 0.3950910265578085
|
||||
7 0.0002545632912247854 -0.00019202725318668095 -0.0007112078778547229 1.4800522749729792 1.8058703404340948 -0.5778414965351256
|
||||
8 0.0018887377488028885 -0.0002473511615838234 0.0008120520191337178 0.18841278062652408 0.3347372075847072 -0.5408605905745774
|
||||
9 0.0002452564077667799 0.00020601300929708606 6.1033299095680186e-05 0.13966147753401867 -0.0005390290197378453 0.6635632318913824
|
||||
10 0.000968244047328249 0.0005529827424647325 -0.00020224034557198784 -0.7235582069719148 -1.9412262416735993 -1.289806869224333
|
||||
11 -0.0017543321990246556 -0.000939796984860897 0.0018048542648271923 -1.5775475529872025 -2.0891633737315023 0.40142307521789933
|
||||
12 -0.0005934853675296159 0.001116191652783757 4.626275649966328e-05 -1.200961814632207 0.4371811217355096 0.43287366246768927
|
||||
13 -0.0007222905985558083 -0.0005767904238661645 0.0006648020330562531 -1.084763819731394 1.1718860080947717 0.2470159472481526
|
||||
14 0.0002573730178578412 -0.00182797610679242 -0.00033107273492769625 -0.510496177490122 0.29118940603730814 0.9195837620128926
|
||||
15 -0.0010092903785878923 0.0011654195253227475 4.0609661125969864e-05 -0.723803934131871 0.07956576746268508 -1.1413793944128399
|
||||
16 -0.0009587558806876301 -0.0004046946607553641 -0.0002343452641922075 0.07373406158203998 -1.3986322243084912 0.4617216556119086
|
||||
|
||||
Bonds
|
||||
|
||||
1 1 1 2
|
||||
2 1 2 3
|
||||
3 1 3 4
|
||||
4 1 4 5
|
||||
5 1 5 6
|
||||
6 1 6 7
|
||||
7 1 7 8
|
||||
8 1 9 10
|
||||
9 1 10 11
|
||||
10 1 11 12
|
||||
11 1 13 14
|
||||
12 1 14 15
|
||||
13 1 15 16
|
||||
|
||||
Ellipsoids
|
||||
|
||||
1 9.999999997766462 9.999999997766462 9.999999997766462 0.9964752158482045 -0.053253555733239796 0.011391163807102514 -0.06380787090289707
|
||||
2 9.999999997766462 9.999999997766462 9.999999997766462 0.9369923833143513 0.11220716044648564 0.06732538499716349 0.3239168400846305
|
||||
3 9.999999997766462 9.999999997766462 9.999999997766462 0.797964932091827 0.14473096354527873 0.18374142699366386 0.5554673737937029
|
||||
4 9.999999997766462 9.999999997766462 9.999999997766462 0.5660864821344559 0.14688275499481052 0.09873742533340191 0.8051226439917721
|
||||
5 9.999999997766462 9.999999997766462 9.999999997766462 0.2533023785125306 0.12062313161679827 0.08583012223905846 0.9559922359911086
|
||||
6 9.999999997766462 9.999999997766462 9.999999997766462 -0.03855807343534716 0.08405913137017908 0.02236505169306371 0.9954632800204194
|
||||
7 9.999999997766462 9.999999997766462 9.999999997766462 -0.45592844330248017 0.1004550065061007 -0.052524745294758785 0.8827679181910482
|
||||
8 9.999999997766462 9.999999997766462 9.999999997766462 0.768021221540491 -0.009582139884533599 0.03658677589040892 -0.63930665074644
|
||||
9 9.999999997766462 9.999999997766462 9.999999997766462 -0.23299975754512345 0.688686395231341 0.6747873944883376 -0.12682324016841584
|
||||
10 9.999999997766462 9.999999997766462 9.999999997766462 -0.24662061871907232 0.8744456399178389 0.39370836087823996 -0.13970261209395163
|
||||
11 9.999999997766462 9.999999997766462 9.999999997766462 -0.087475900850909 0.977367602388229 0.14493549113095577 -0.12686307572668784
|
||||
12 9.999999997766462 9.999999997766462 9.999999997766462 -0.03181169300779214 0.9634374984140112 -0.2442360692534371 -0.10547485630879185
|
||||
13 9.999999997766462 9.999999997766462 9.999999997766462 -0.032786070696572266 0.7922941528811777 -0.6084214170523915 -0.03191282109962717
|
||||
14 9.999999997766462 9.999999997766462 9.999999997766462 0.047188686288341455 0.6316396208287698 -0.7737349519945348 0.011783095844627799
|
||||
15 9.999999997766462 9.999999997766462 9.999999997766462 -0.05869980642620335 -0.34229358203414423 0.9376740835056508 0.012519965878508689
|
||||
16 9.999999997766462 9.999999997766462 9.999999997766462 -0.08582818143150042 0.0008707732197394232 0.9939540921464659 -0.0684691735853161
|
||||
@ -0,0 +1,73 @@
|
||||
# LAMMPS input file in real units via oxdna lj2real.py, date 2024-05-19
|
||||
variable number equal 2
|
||||
variable ofreq equal 1000
|
||||
variable efreq equal 1000
|
||||
variable T equal 300.0
|
||||
variable rhos equal 0.2
|
||||
|
||||
units real
|
||||
|
||||
dimension 3
|
||||
|
||||
newton on
|
||||
|
||||
boundary p p p
|
||||
|
||||
atom_style hybrid bond ellipsoid oxdna
|
||||
atom_modify sort 0 8.518
|
||||
|
||||
# Pair interactions require lists of neighbours to be calculated
|
||||
neighbor 17.036 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
read_data data.duplex2
|
||||
|
||||
set atom * mass 315.8376
|
||||
|
||||
group all type 1 4
|
||||
|
||||
# oxDNA2 bond interactions - FENE backbone
|
||||
bond_style oxdna2/fene
|
||||
bond_coeff * 11.92337812042065 2.1295 6.4430152
|
||||
special_bonds lj 0 1 1
|
||||
|
||||
# oxDNA2 pair interactions
|
||||
pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
|
||||
pair_coeff * * oxdna2/excv 11.92337812042065 5.9626 5.74965 11.92337812042065 4.38677 4.259 11.92337812042065 2.81094 2.72576
|
||||
pair_coeff * * oxdna2/stk seqav ${T} 8.06199211612242 0.005309213 0.70439070204273 3.4072 7.6662 2.72576 6.3885 1.3 0.0 0.8 0.9 0.0 0.95 0.9 0.0 0.95 2.0 0.65 2.0 0.65
|
||||
pair_coeff * * oxdna2/hbond seqav 0.0 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0.0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45
|
||||
pair_coeff 1 4 oxdna2/hbond seqav 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45
|
||||
pair_coeff 2 3 oxdna2/hbond seqav 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45
|
||||
pair_coeff * * oxdna2/xstk 3.9029021145006 4.89785 5.74965 4.21641 5.57929 2.25 0.791592654 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
|
||||
pair_coeff * * oxdna2/coaxstk 4.80673207785863 3.4072 5.1108 1.87396 4.94044 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793
|
||||
pair_coeff * * oxdna2/dh ${T} ${rhos} 0.815
|
||||
|
||||
# NVE ensemble
|
||||
fix 1 all nve/asphere
|
||||
fix 2 all langevin ${T} ${T} 4265.0 457145 angmom 10
|
||||
|
||||
timestep 0.01706
|
||||
|
||||
#comm_style tiled
|
||||
fix 3 all balance 1000 1.03 shift xyz 10 1.03
|
||||
comm_modify cutoff 32.4
|
||||
|
||||
compute quat all property/atom quatw quati quatj quatk
|
||||
|
||||
compute erot all erotate/asphere
|
||||
compute ekin all ke
|
||||
compute epot all pe
|
||||
variable erot equal c_erot
|
||||
variable ekin equal c_ekin
|
||||
variable epot equal c_epot
|
||||
variable etot equal c_erot+c_ekin+c_epot
|
||||
fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
|
||||
|
||||
dump out all custom ${ofreq} out.${number}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz
|
||||
dump_modify out sort id
|
||||
dump_modify out format line "%d %d %d %22.15le %22.15le %22.15le %d %d %d %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le"
|
||||
|
||||
run 1000000
|
||||
|
||||
write_data last_config.${number}.* nocoeff
|
||||
#write_restart last_config.${number}.*
|
||||
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
@ -0,0 +1,68 @@
|
||||
LAMMPS data file in real units via oxdna lj2real.py, date 2024-05-19
|
||||
|
||||
10 atoms
|
||||
4 atom types
|
||||
8 bonds
|
||||
1 bond types
|
||||
10 ellipsoids
|
||||
|
||||
-170 170 xlo xhi
|
||||
-170 170 ylo yhi
|
||||
-170 170 zlo zhi
|
||||
|
||||
Masses
|
||||
|
||||
1 100.0278
|
||||
2 100.0278
|
||||
3 100.0278
|
||||
4 100.0278
|
||||
|
||||
Atoms # hybrid
|
||||
|
||||
1 1 -0.9600635673395586 -6.697372578532395 11.214288461530149 1 1 0.016231479325760585 0 0 0
|
||||
2 2 -1.371418484333729 -8.644426415489871 15.09830243650489 1 1 0.016231479325760585 0 0 0
|
||||
3 3 -0.6216529396853785 -10.27130427566052 18.871948109873205 1 1 0.016231479325760585 0 0 0
|
||||
4 4 1.779062937600471 -10.807909849707325 23.24831121047697 1 1 0.016231479325760585 0 0 0
|
||||
5 1 4.239477379859167 -10.116984578731293 26.59145222824391 1 1 0.016231479325760585 0 0 0
|
||||
6 4 -1.9327071764636017 -1.6150385295751968 26.477847842079502 2 1 0.016231479325760585 0 0 0
|
||||
7 1 -0.2983880618807194 -0.9579116659377174 23.010952595199885 2 1 0.016231479325760585 0 0 0
|
||||
8 2 2.1503419307040095 -0.31467499729662424 19.779605638337472 2 1 0.016231479325760585 0 0 0
|
||||
9 3 5.687077844288683 -1.6585607691903788 17.32600745817322 2 1 0.016231479325760585 0 0 0
|
||||
10 4 7.960942109870774 -4.424349635235229 15.853866095654556 2 1 0.016231479325760585 0 0 0
|
||||
|
||||
Velocities
|
||||
|
||||
1 0.003670260004547261 -0.001065537256202598 0.00019820771627082902 2.190783710921869 -2.4582417153465035 1.7715963770507672
|
||||
2 0.002291113608335764 0.0007728773438117204 0.002296672286413572 -0.40551125639613556 -0.12256940476096484 0.7114827747471555
|
||||
3 -0.0004997750377219465 -0.0006770677373491773 -0.0006775964298166731 2.179995735254803 3.7414175740175044 -1.7280709663891953
|
||||
4 -0.00015182185791796758 -4.553427726427798e-05 0.001445301171404135 -0.9443175316300753 1.9770932892489974 -0.3048781148297085
|
||||
5 0.00010888231798112065 -0.0017696699496284707 0.002217080679988605 -0.08456353584305179 0.035965271955914695 -0.7051030632137099
|
||||
6 0.0002936592731756661 -0.0011965505946877099 0.0004708407813130548 -0.7164699339101465 -1.1698888787077064 2.094408810880699
|
||||
7 -2.1364103955982793e-05 5.577692626680783e-05 -0.0005335687118188998 1.5034116933686936 -2.4596844236201743 0.7286296966602159
|
||||
8 -0.002835367576168593 -0.00028136761767332186 -0.0006160127733736687 -0.26771671594599533 -2.360332797207871 -1.6798429613010255
|
||||
9 0.00037413027551487407 0.001890740851504142 0.0005563994572100851 -1.512871512517161 -1.4691678195901636 -2.245351079807635
|
||||
10 -0.0024375187569690418 -0.000550577454043892 0.000971907386756427 0.4399243786321997 1.6207637079017971 1.0900899238856114
|
||||
|
||||
Bonds
|
||||
|
||||
1 1 1 2
|
||||
2 1 2 3
|
||||
3 1 3 4
|
||||
4 1 4 5
|
||||
5 1 6 7
|
||||
6 1 7 8
|
||||
7 1 8 9
|
||||
8 1 9 10
|
||||
|
||||
Ellipsoids
|
||||
|
||||
1 26.93628110931426 26.93628110931426 26.93628110931426 0.9824438652148015 -0.023183015026523597 -0.18238525095550406 0.031657854475291056
|
||||
2 26.93628110931426 26.93628110931426 26.93628110931426 0.9303156820429525 0.02962373336578937 -0.07607439157272995 0.3575581814380256
|
||||
3 26.93628110931426 26.93628110931426 26.93628110931426 0.7912072782182723 -0.043679545103099016 -0.05996218100443608 0.6070318583758278
|
||||
4 26.93628110931426 26.93628110931426 26.93628110931426 0.6531869542452552 -0.03659000162837596 0.004181596561545229 0.7563005281201641
|
||||
5 26.93628110931426 26.93628110931426 26.93628110931426 0.3249781771672557 0.06207197535108856 0.03689277251937633 0.9429608568635791
|
||||
6 26.93628110931426 26.93628110931426 26.93628110931426 0.08029535222204207 0.8726095530830543 -0.46831094470633033 -0.11309325067392484
|
||||
7 26.93628110931426 26.93628110931426 26.93628110931426 -0.1303991484205687 0.7764383491760718 -0.6081660772848121 0.10135864274905797
|
||||
8 26.93628110931426 26.93628110931426 26.93628110931426 -0.14971034142173664 0.5769499085020084 -0.7973230447846137 0.09482393688465168
|
||||
9 26.93628110931426 26.93628110931426 26.93628110931426 0.21130729744233523 -0.37917864508185584 0.8946270178621702 -0.10590221939385809
|
||||
10 26.93628110931426 26.93628110931426 26.93628110931426 0.34278400171414436 0.15185237372800306 0.9252984668160771 0.05712032974191834
|
||||
@ -0,0 +1,73 @@
|
||||
# LAMMPS input file in real units via oxdna lj2real.py, date 2024-05-19
|
||||
variable number equal 3
|
||||
variable ofreq equal 1000
|
||||
variable efreq equal 1000
|
||||
variable T equal 300.0
|
||||
variable rhos equal 0.2
|
||||
|
||||
units real
|
||||
|
||||
dimension 3
|
||||
|
||||
newton on
|
||||
|
||||
boundary p p p
|
||||
|
||||
atom_style hybrid bond ellipsoid oxdna
|
||||
atom_modify sort 0 8.518
|
||||
|
||||
# Pair interactions require lists of neighbours to be calculated
|
||||
neighbor 17.036 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
read_data data.duplex3
|
||||
|
||||
set atom * mass 100.0278
|
||||
|
||||
group all type 1 4
|
||||
|
||||
# oxDNA2 bond interactions - FENE backbone
|
||||
bond_style oxdna2/fene
|
||||
bond_coeff * 11.92337812042065 2.1295 6.4430152
|
||||
special_bonds lj 0 1 1
|
||||
|
||||
# oxDNA2 pair interactions
|
||||
pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
|
||||
pair_coeff * * oxdna2/excv 11.92337812042065 5.9626 5.74965 11.92337812042065 4.38677 4.259 11.92337812042065 2.81094 2.72576
|
||||
pair_coeff * * oxdna2/stk seqdep ${T} 8.06199211612242 0.005309213 0.70439070204273 3.4072 7.6662 2.72576 6.3885 1.3 0.0 0.8 0.9 0.0 0.95 0.9 0.0 0.95 2.0 0.65 2.0 0.65
|
||||
pair_coeff * * oxdna2/hbond seqdep 0.0 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0.0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45
|
||||
pair_coeff 1 4 oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45
|
||||
pair_coeff 2 3 oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45
|
||||
pair_coeff * * oxdna2/xstk 3.9029021145006 4.89785 5.74965 4.21641 5.57929 2.25 0.791592654 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
|
||||
pair_coeff * * oxdna2/coaxstk 4.80673207785863 3.4072 5.1108 1.87396 4.94044 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793
|
||||
pair_coeff * * oxdna2/dh ${T} ${rhos} 0.815
|
||||
|
||||
# NVE ensemble
|
||||
fix 1 all nve/asphere
|
||||
#fix 2 all langevin ${T} ${T} 4265.0 457145 angmom 10
|
||||
|
||||
timestep 0.01706
|
||||
|
||||
#comm_style tiled
|
||||
fix 3 all balance 1000 1.03 shift xyz 10 1.03
|
||||
comm_modify cutoff 32.4
|
||||
|
||||
compute quat all property/atom quatw quati quatj quatk
|
||||
|
||||
compute erot all erotate/asphere
|
||||
compute ekin all ke
|
||||
compute epot all pe
|
||||
variable erot equal c_erot
|
||||
variable ekin equal c_ekin
|
||||
variable epot equal c_epot
|
||||
variable etot equal c_erot+c_ekin+c_epot
|
||||
fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
|
||||
|
||||
dump out all custom ${ofreq} out.${number}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz
|
||||
dump_modify out sort id
|
||||
dump_modify out format line "%d %d %d %22.15le %22.15le %22.15le %d %d %d %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le"
|
||||
|
||||
run 1000000
|
||||
|
||||
write_data last_config.${number}.* nocoeff
|
||||
#write_restart last_config.${number}.*
|
||||
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
@ -0,0 +1,68 @@
|
||||
LAMMPS data file in real units via oxdna lj2real.py, date 2024-05-19
|
||||
|
||||
10 atoms
|
||||
4 atom types
|
||||
8 bonds
|
||||
1 bond types
|
||||
10 ellipsoids
|
||||
|
||||
-170 170 xlo xhi
|
||||
-170 170 ylo yhi
|
||||
-170 170 zlo zhi
|
||||
|
||||
Masses
|
||||
|
||||
1 315.8376
|
||||
2 315.8376
|
||||
3 315.8376
|
||||
4 315.8376
|
||||
|
||||
Atoms # hybrid
|
||||
|
||||
1 1 -2.8740969069282687 -3.723118600434732 5.494693518792015 1 1 1.0016462505133576 0 0 0
|
||||
2 2 -2.7379071878387986 -6.079929519421481 10.066032484018534 1 1 1.0016462505133576 0 0 0
|
||||
3 3 -1.110437385073819 -7.791537941948432 13.848676172779387 1 1 1.0016462505133576 0 0 0
|
||||
4 4 1.4306089998272526 -8.354886654263622 17.79828313773629 1 1 1.0016462505133576 0 0 0
|
||||
5 1 3.9498326729322186 -6.646891787969407 20.657842369456382 1 1 1.0016462505133576 0 0 0
|
||||
6 4 -3.801540967989063 0.7719150486872158 21.01300417274477 2 1 1.0016462505133576 0 0 0
|
||||
7 1 -0.287657468030243 1.787063409177335 17.702181979507532 2 1 1.0016462505133576 0 0 0
|
||||
8 2 2.8086617684512323 1.5040732709582532 14.656350509768911 2 1 1.0016462505133576 0 0 0
|
||||
9 3 5.165059071666839 0.3988634556159852 10.50699529001116 2 1 1.0016462505133576 0 0 0
|
||||
10 4 6.817789789050184 -3.1038996716078557 8.419212766646357 2 1 1.0016462505133576 0 0 0
|
||||
|
||||
Velocities
|
||||
|
||||
1 0.0015993537866009029 -0.000680681865016988 -0.00014678467473993874 1.3034875452014287 -0.6725260292370423 1.5263182328899618
|
||||
2 0.0008422431968202534 -0.0002471920411024751 0.0007894382186365997 -0.32615096872390803 -0.0034351199136194157 -0.9136220137417161
|
||||
3 -0.0011446153381118452 0.00041850425643063176 -0.00045926941555484915 1.7184317758530245 2.6050996986101502 -0.47065934236730145
|
||||
4 -0.0011077496385743138 0.0002472924939324634 -0.00034633314311123244 -0.5778245520276679 1.752085001878762 -0.24048635097513535
|
||||
5 0.0004072478403200556 -0.0012804934445473403 0.0008610591638760516 0.23142339993018143 0.3972766524238825 1.363641236078021
|
||||
6 0.00017968178785700138 -0.00024308968845109275 0.00014280408309295725 0.1704955558294103 -1.3525913126172677 1.5501424653239764
|
||||
7 -4.108556803115003e-05 0.00023724044475488887 -0.00013843701960263193 0.7809156374181498 -2.1218743676572576 0.2975087875146955
|
||||
8 -0.00035835254321313353 0.0008579277312926632 0.0019500603503724006 -0.711656157643413 -2.0351916264105014 -0.7613827970610736
|
||||
9 -0.0008730894357027041 -0.00039026927657647716 0.0002796967510539106 -1.193834703375802 1.023301140813147 -1.8342354268493246
|
||||
10 0.0009421885758929626 -0.0005326396944231774 0.0006296458639527654 -0.24420734152643714 1.5633648178267814 0.6376075187926279
|
||||
|
||||
Bonds
|
||||
|
||||
1 1 1 2
|
||||
2 1 2 3
|
||||
3 1 3 4
|
||||
4 1 4 5
|
||||
5 1 6 7
|
||||
6 1 7 8
|
||||
7 1 8 9
|
||||
8 1 9 10
|
||||
|
||||
Ellipsoids
|
||||
|
||||
1 9.999999997766462 9.999999997766462 9.999999997766462 0.9890278201757743 0.01779228232037064 -0.14337734159225404 0.030827642240801516
|
||||
2 9.999999997766462 9.999999997766462 9.999999997766462 0.939687458852748 0.04174166924055095 -0.023337773785056866 0.338674565089608
|
||||
3 9.999999997766462 9.999999997766462 9.999999997766462 0.8210113150655425 0.03012140921736572 0.017666019956944813 0.5698429897612057
|
||||
4 9.999999997766462 9.999999997766462 9.999999997766462 0.6623662858285051 -0.028186343967346823 0.022942552517501488 0.7482981175276918
|
||||
5 9.999999997766462 9.999999997766462 9.999999997766462 0.3601488726765216 0.0513614985821682 0.0724224158335286 0.9286602067807472
|
||||
6 9.999999997766462 9.999999997766462 9.999999997766462 0.11941234710084649 0.9244660117493703 -0.35317942248051865 -0.07979711784524246
|
||||
7 9.999999997766462 9.999999997766462 9.999999997766462 -0.17949125421205164 0.7412884899431119 -0.6379094464220707 0.1065166771202199
|
||||
8 9.999999997766462 9.999999997766462 9.999999997766462 -0.10483691088405202 0.5508895999584645 -0.8250090480220789 0.06992811634525403
|
||||
9 9.999999997766462 9.999999997766462 9.999999997766462 0.07777239911646 -0.3724087549185288 0.9103052384821374 -0.1631181963720798
|
||||
10 9.999999997766462 9.999999997766462 9.999999997766462 0.16279109707978262 0.027148630125149613 0.9849325709665359 -0.0516705065113425
|
||||
@ -0,0 +1,74 @@
|
||||
# LAMMPS input file in real units via oxdna lj2real.py, date 2024-05-19
|
||||
variable number equal 1
|
||||
variable ofreq equal 1000
|
||||
variable efreq equal 1000
|
||||
variable T equal 300.0
|
||||
variable rhos equal 0.2
|
||||
|
||||
units real
|
||||
|
||||
dimension 3
|
||||
|
||||
newton on
|
||||
|
||||
boundary p p p
|
||||
|
||||
atom_style hybrid bond ellipsoid oxdna
|
||||
atom_modify sort 0 8.518
|
||||
|
||||
# Pair interactions require lists of neighbours to be calculated
|
||||
neighbor 17.036 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
read_data data.duplex1
|
||||
|
||||
set atom * mass 315.8376
|
||||
|
||||
group all type 1 4
|
||||
|
||||
# oxDNA2 bond interactions - FENE backbone
|
||||
bond_style oxdna2/fene
|
||||
bond_coeff * oxdna2_real.cgdna
|
||||
special_bonds fene
|
||||
|
||||
# oxDNA2 pair interactions
|
||||
pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
|
||||
pair_coeff * * oxdna2/excv oxdna2_real.cgdna
|
||||
pair_coeff * * oxdna2/stk seqav 300.0 8.06199211612242 0.005309213 oxdna2_real.cgdna
|
||||
pair_coeff * * oxdna2/hbond seqav oxdna2_real.cgdna
|
||||
pair_coeff 1 4 oxdna2/hbond seqav oxdna2_real.cgdna
|
||||
pair_coeff 2 3 oxdna2/hbond seqav oxdna2_real.cgdna
|
||||
pair_coeff * * oxdna2/xstk oxdna2_real.cgdna
|
||||
pair_coeff * * oxdna2/coaxstk oxdna2_real.cgdna
|
||||
pair_coeff * * oxdna2/dh 300.0 0.5 oxdna2_real.cgdna
|
||||
|
||||
|
||||
# NVE ensemble
|
||||
fix 1 all nve/asphere
|
||||
#fix 2 all langevin ${T} ${T} 4265.0 457145 angmom 10
|
||||
|
||||
timestep 0.01706
|
||||
|
||||
#comm_style tiled
|
||||
fix 3 all balance 1000 1.03 shift xyz 10 1.03
|
||||
comm_modify cutoff 32.4
|
||||
|
||||
compute quat all property/atom quatw quati quatj quatk
|
||||
|
||||
compute erot all erotate/asphere
|
||||
compute ekin all ke
|
||||
compute epot all pe
|
||||
variable erot equal c_erot
|
||||
variable ekin equal c_ekin
|
||||
variable epot equal c_epot
|
||||
variable etot equal c_erot+c_ekin+c_epot
|
||||
fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
|
||||
|
||||
dump out all custom ${ofreq} out.${number}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz
|
||||
dump_modify out sort id
|
||||
dump_modify out format line "%d %d %d %22.15le %22.15le %22.15le %d %d %d %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le"
|
||||
|
||||
run 1000000
|
||||
|
||||
write_data last_config.${number}.* nocoeff
|
||||
#write_restart last_config.${number}.*
|
||||
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
@ -0,0 +1 @@
|
||||
../../../../../../../potentials/oxdna2_real.cgdna
|
||||
@ -0,0 +1,132 @@
|
||||
LAMMPS data file in real units via oxdna lj2real.py, date 2024-05-19
|
||||
|
||||
26 atoms
|
||||
4 atom types
|
||||
24 bonds
|
||||
1 bond types
|
||||
26 ellipsoids
|
||||
|
||||
-170 170 xlo xhi
|
||||
-170 170 ylo yhi
|
||||
-170 170 zlo zhi
|
||||
|
||||
Masses
|
||||
|
||||
1 315.8376
|
||||
2 315.8376
|
||||
3 315.8376
|
||||
4 315.8376
|
||||
|
||||
Atoms # hybrid
|
||||
|
||||
1 1 -5.088903454828145 -4.022006630398617 0.979450832492054 1 1 1.0016462505133576 0 0 0
|
||||
2 2 -3.073273348143933 -6.886121795405585 4.2637967191149935 1 1 1.0016462505133576 0 0 0
|
||||
3 3 -1.6015249052848957 -7.954971258517993 7.983259491779774 1 1 1.0016462505133576 0 0 0
|
||||
4 4 1.6004494372303046 -7.502206000462345 11.142183230976523 1 1 1.0016462505133576 0 0 0
|
||||
5 1 3.9762269824284777 -5.378694720128274 14.092706034736517 1 1 1.0016462505133576 0 0 0
|
||||
6 2 5.244098183685422 -2.0736999117014334 17.034635513902522 1 1 1.0016462505133576 0 0 0
|
||||
7 3 4.66434547759629 0.9057195140116471 20.406471315843888 1 1 1.0016462505133576 0 0 0
|
||||
8 4 3.3770131096003007 2.884613516099349 24.32212902640886 1 1 1.0016462505133576 0 0 0
|
||||
9 1 0.7795485088930724 2.8596780468864993 27.93316866219941 1 1 1.0016462505133576 0 0 0
|
||||
10 2 -2.220644638122167 1.9976911283301424 30.852747566202943 1 1 1.0016462505133576 0 0 0
|
||||
11 3 -3.752108563283866 -0.36118973532266224 34.56060757623137 1 1 1.0016462505133576 0 0 0
|
||||
12 4 -4.0981351277114095 -3.3336637232155737 38.03472139175804 1 1 1.0016462505133576 0 0 0
|
||||
13 1 -2.580860807366316 -5.296690457458744 41.65233354663661 1 1 1.0016462505133576 0 0 0
|
||||
14 4 3.11235736590125 3.9787921540654274 41.61858344700847 2 1 1.0016462505133576 0 0 0
|
||||
15 1 4.972174868431865 1.22026293032667 39.080053199424356 2 1 1.0016462505133576 0 0 0
|
||||
16 2 6.193349083696695 -1.843990009872412 35.70127548826449 2 1 1.0016462505133576 0 0 0
|
||||
17 3 4.85045978654294 -5.086115266816092 32.287814957190825 2 1 1.0016462505133576 0 0 0
|
||||
18 4 2.7413887948469777 -6.6667612407190076 28.945688671744993 2 1 1.0016462505133576 0 0 0
|
||||
19 1 0.23801913694460985 -6.962572452460229 24.638294488589953 2 1 1.0016462505133576 0 0 0
|
||||
20 2 -2.929295143505978 -5.793156995357843 22.155368377440084 2 1 1.0016462505133576 0 0 0
|
||||
21 3 -4.874287161624311 -2.6868984302083723 19.162406167006097 2 1 1.0016462505133576 0 0 0
|
||||
22 4 -4.466038023713098 -0.16009445500929992 14.199167217812603 2 1 1.0016462505133576 0 0 0
|
||||
23 1 -3.805032901797115 1.3047989425274054 9.939919176722297 2 1 1.0016462505133576 0 0 0
|
||||
24 2 -0.3645313828582167 2.0504253339486334 6.749830838323167 2 1 1.0016462505133576 0 0 0
|
||||
25 3 2.8696234661228 1.1843850873648512 3.5779840008575166 2 1 1.0016462505133576 0 0 0
|
||||
26 4 4.584052070339748 -2.4162961106383802 0.4178747538604132 2 1 1.0016462505133576 0 0 0
|
||||
|
||||
Velocities
|
||||
|
||||
1 -0.0007092826233374404 -0.0011683182237858898 0.0009345415878891811 -0.19711297351977997 0.3471662755040702 1.1876949496899232
|
||||
2 0.0001692806579311005 0.001454411904318072 -0.0009132068521112497 0.40085230919108755 -0.18887849087800404 0.047091827325408245
|
||||
3 0.00026721094548725233 -0.0018474107413693995 -7.33687581476124e-05 0.46267958346439353 1.0098887515959383 0.6393407481151142
|
||||
4 0.0005530692647148845 6.276724836348722e-05 0.0011760622369354724 0.485473149019376 -1.016731064060453 0.4763136256195711
|
||||
5 0.0010959077967915062 -0.002073578927849095 0.0009200279724368436 1.0623586979165884 1.065939836735458 -1.5037672467577814
|
||||
6 -0.0011992989214254961 -0.0008200232774176946 -1.878586889584186e-05 0.2637939462292815 0.9503989065450423 -1.6260870297579495
|
||||
7 0.0006177535901987009 0.000518919774167013 0.0003998839732602718 -0.6408171281169938 0.36348341926995353 -1.375803360797847
|
||||
8 0.00016059142531900045 -0.0006450606532728585 0.0008669204672450051 -0.7477778258878353 0.47361246994539824 -0.5810846842200627
|
||||
9 8.231216517048786e-05 6.015188190262039e-05 6.125792756154739e-05 -0.4607197796707098 0.5637456934375974 0.26087415190460156
|
||||
10 -0.000500147138046807 -0.000463066044342822 0.000355851169196805 -0.36328886676626787 -0.43369687106567045 0.5273136714151697
|
||||
11 0.0007757175683907118 -8.926233267161596e-05 -0.0008385947169209714 -0.4808110547195639 0.46086842856246785 -1.2339214306000716
|
||||
12 -0.001263650191118318 0.00028219137594863816 -0.0014126973797773772 0.3775783079049196 -0.1807429862945671 2.0452684483124046
|
||||
13 -3.2579866050976174e-05 0.0002635521160422669 0.0004611578260851882 -0.7261457161482728 -0.9102614938022983 -0.950223070000176
|
||||
14 -0.0004505866261683952 0.0009690259297353478 -0.0013620790360894626 0.7053189033188233 0.2384556381419323 0.771670025066328
|
||||
15 0.0011631309106043411 0.00044570587091719976 8.76640977124226e-05 0.6336939456886027 0.23680623944908769 0.16348552253269122
|
||||
16 -6.374073980270027e-05 -0.0002931008886831666 0.001121388312515121 -0.22078626344978855 0.4828157321900567 -1.5155692478249987
|
||||
17 -0.0010186027342478764 -0.002155869929612435 -0.0002602846290421834 -0.7045426361887308 -0.35130535920917716 -1.3344634305851248
|
||||
18 0.0013185658893551267 2.047723112341404e-05 -0.0005696586063762746 -1.6060222297755182 0.09031942024852611 0.9877781291576422
|
||||
19 -0.0014036986693625635 0.0012719382904391608 1.897600955961397e-05 0.9208051089916969 -1.6695360996503725 0.9680334678576618
|
||||
20 -0.0017040889747209288 0.00025337668854442876 -0.0001691840039087206 -0.5820811149791364 -0.6584676155867104 -0.13895286467266474
|
||||
21 -0.0012832301288169161 0.00023432762658239688 0.0004175391014650396 -0.368479743293301 -0.13070387294699928 -0.7972536298008709
|
||||
22 0.000425865764618422 0.0005323528439718917 -0.00037084207215630813 -1.987484231007066 -0.8187640783546725 0.8567029127863278
|
||||
23 -0.0004662057261624694 -0.0009522140435800978 0.0009625566807134454 0.07570418552326717 -1.5530387610102858 1.0623583182518839
|
||||
24 -0.0008020353772621954 0.0006130763545177365 0.000256600283460346 -0.4133480645752746 -1.123177366593782 0.34895664453469977
|
||||
25 -0.0007357778484794694 0.0004842720240985607 -0.0010361169830474496 0.23875324331203535 -0.5925750420871833 0.1484289925046781
|
||||
26 -0.000301663155222858 0.001775092432198598 -0.0009822913284976214 0.0628202961121918 0.11750852756815655 -0.8762490863383418
|
||||
|
||||
Bonds
|
||||
|
||||
1 1 1 2
|
||||
2 1 2 3
|
||||
3 1 3 4
|
||||
4 1 4 5
|
||||
5 1 5 6
|
||||
6 1 6 7
|
||||
7 1 7 8
|
||||
8 1 8 9
|
||||
9 1 9 10
|
||||
10 1 10 11
|
||||
11 1 11 12
|
||||
12 1 12 13
|
||||
13 1 14 15
|
||||
14 1 15 16
|
||||
15 1 16 17
|
||||
16 1 17 18
|
||||
17 1 18 19
|
||||
18 1 19 20
|
||||
19 1 20 21
|
||||
20 1 21 22
|
||||
21 1 22 23
|
||||
22 1 23 24
|
||||
23 1 24 25
|
||||
24 1 25 26
|
||||
|
||||
Ellipsoids
|
||||
|
||||
1 9.999999997766462 9.999999997766462 9.999999997766462 0.9970278940278272 0.0014876174054512252 0.0750547523448584 0.017319055267040844
|
||||
2 9.999999997766462 9.999999997766462 9.999999997766462 0.9059171712388804 0.007913225291438054 0.04634256838354512 0.42083705406683053
|
||||
3 9.999999997766462 9.999999997766462 9.999999997766462 0.7657426991864452 0.028071560533125216 0.13224385975981257 0.6287779160305484
|
||||
4 9.999999997766462 9.999999997766462 9.999999997766462 0.5238981696613685 0.0516703526741727 0.1609645534282743 0.8348360887142046
|
||||
5 9.999999997766462 9.999999997766462 9.999999997766462 0.30973290897949424 0.0750672191209306 0.23962885621884192 0.9170651279902646
|
||||
6 9.999999997766462 9.999999997766462 9.999999997766462 -0.050269263744563454 0.08142241031464711 0.09584085715741358 0.9907865170259763
|
||||
7 9.999999997766462 9.999999997766462 9.999999997766462 -0.3805122714271814 0.08965734720629535 0.057827749665601925 0.9186010683391725
|
||||
8 9.999999997766462 9.999999997766462 9.999999997766462 -0.6066322463100545 0.015286960797006149 0.035984536832974555 0.7940206166563465
|
||||
9 9.999999997766462 9.999999997766462 9.999999997766462 0.771660293819677 0.02607541526374929 -0.08047223278265907 -0.6303845520092687
|
||||
10 9.999999997766462 9.999999997766462 9.999999997766462 0.9119628434851113 0.03686258000931541 -0.11017000132786052 -0.3934812487336936
|
||||
11 9.999999997766462 9.999999997766462 9.999999997766462 0.9917294290821066 0.05835078551401739 -0.08073737536574405 -0.08092837290732445
|
||||
12 9.999999997766462 9.999999997766462 9.999999997766462 0.9763527785523285 0.06753089597617556 0.004847281702108697 0.205307899901351
|
||||
13 9.999999997766462 9.999999997766462 9.999999997766462 0.8553397145502984 0.1399133966151149 0.07233200118835512 0.49354462388392356
|
||||
14 9.999999997766462 9.999999997766462 9.999999997766462 0.014416326682630282 -0.533642571147991 0.8442695396252617 0.04718813669228716
|
||||
15 9.999999997766462 9.999999997766462 9.999999997766462 0.14095892784917538 -0.2201285495070387 0.9406003462562982 -0.21666792788520955
|
||||
16 9.999999997766462 9.999999997766462 9.999999997766462 0.07323967796304806 0.05035907488974361 0.963136526452943 -0.2539053850556888
|
||||
17 9.999999997766462 9.999999997766462 9.999999997766462 0.030254986187638885 0.39195467212588947 0.9164794947567249 -0.07430684019611289
|
||||
18 9.999999997766462 9.999999997766462 9.999999997766462 -0.03080283760241768 0.6526511470205414 0.7481495879677094 -0.11562810865943304
|
||||
19 9.999999997766462 9.999999997766462 9.999999997766462 -0.09450197979153381 0.7469150592813072 0.6556128255138505 -0.0579576833217777
|
||||
20 9.999999997766462 9.999999997766462 9.999999997766462 -0.12903334341475137 0.9222523214328698 0.3501336268694509 -0.10103214950765672
|
||||
21 9.999999997766462 9.999999997766462 9.999999997766462 -0.0069954457806870336 0.9888131084284681 -0.09413955816471489 -0.11548785185859346
|
||||
22 9.999999997766462 9.999999997766462 9.999999997766462 0.029336230851923526 0.9805894852440379 -0.19236800606724952 -0.02404573205262194
|
||||
23 9.999999997766462 9.999999997766462 9.999999997766462 0.03080980270092377 0.872234086776475 -0.4869211139732921 0.03415088124407873
|
||||
24 9.999999997766462 9.999999997766462 9.999999997766462 0.007237815450514786 0.690265186998662 -0.7210993183911308 0.05913847022922672
|
||||
25 9.999999997766462 9.999999997766462 9.999999997766462 0.06694683426684143 -0.46894411325316443 0.8712038661029582 -0.12889283810247346
|
||||
26 9.999999997766462 9.999999997766462 9.999999997766462 0.07581973147109407 -0.10215114654759445 0.9759556607577902 -0.17699451916228467
|
||||
@ -0,0 +1,136 @@
|
||||
LAMMPS data file in real units via oxdna lj2real.py, date 2024-05-19
|
||||
|
||||
26 atoms
|
||||
8 atom types
|
||||
24 bonds
|
||||
1 bond types
|
||||
26 ellipsoids
|
||||
|
||||
-170 170 xlo xhi
|
||||
-170 170 ylo yhi
|
||||
-170 170 zlo zhi
|
||||
|
||||
Masses
|
||||
|
||||
1 315.8376
|
||||
2 315.8376
|
||||
3 315.8376
|
||||
4 315.8376
|
||||
5 315.8376
|
||||
6 315.8376
|
||||
7 315.8376
|
||||
8 315.8376
|
||||
|
||||
Atoms # hybrid
|
||||
|
||||
1 1 -5.088903454828145 -4.022006630398617 0.979450832492054 1 1 1.0016462505133576 0 0 0
|
||||
2 2 -3.073273348143933 -6.886121795405585 4.2637967191149935 1 1 1.0016462505133576 0 0 0
|
||||
3 3 -1.6015249052848957 -7.954971258517993 7.983259491779774 1 1 1.0016462505133576 0 0 0
|
||||
4 4 1.6004494372303046 -7.502206000462345 11.142183230976523 1 1 1.0016462505133576 0 0 0
|
||||
5 5 3.9762269824284777 -5.378694720128274 14.092706034736517 1 1 1.0016462505133576 0 0 0
|
||||
6 6 5.244098183685422 -2.0736999117014334 17.034635513902522 1 1 1.0016462505133576 0 0 0
|
||||
7 7 4.66434547759629 0.9057195140116471 20.406471315843888 1 1 1.0016462505133576 0 0 0
|
||||
8 8 3.3770131096003007 2.884613516099349 24.32212902640886 1 1 1.0016462505133576 0 0 0
|
||||
9 1 0.7795485088930724 2.8596780468864993 27.93316866219941 1 1 1.0016462505133576 0 0 0
|
||||
10 2 -2.220644638122167 1.9976911283301424 30.852747566202943 1 1 1.0016462505133576 0 0 0
|
||||
11 7 -3.752108563283866 -0.36118973532266224 34.56060757623137 1 1 1.0016462505133576 0 0 0
|
||||
12 8 -4.0981351277114095 -3.3336637232155737 38.03472139175804 1 1 1.0016462505133576 0 0 0
|
||||
13 1 -2.580860807366316 -5.296690457458744 41.65233354663661 1 1 1.0016462505133576 0 0 0
|
||||
14 4 3.11235736590125 3.9787921540654274 41.61858344700847 2 1 1.0016462505133576 0 0 0
|
||||
15 5 4.972174868431865 1.22026293032667 39.080053199424356 2 1 1.0016462505133576 0 0 0
|
||||
16 6 6.193349083696695 -1.843990009872412 35.70127548826449 2 1 1.0016462505133576 0 0 0
|
||||
17 3 4.85045978654294 -5.086115266816092 32.287814957190825 2 1 1.0016462505133576 0 0 0
|
||||
18 4 2.7413887948469777 -6.6667612407190076 28.945688671744993 2 1 1.0016462505133576 0 0 0
|
||||
19 5 0.23801913694460985 -6.962572452460229 24.638294488589953 2 1 1.0016462505133576 0 0 0
|
||||
20 6 -2.929295143505978 -5.793156995357843 22.155368377440084 2 1 1.0016462505133576 0 0 0
|
||||
21 7 -4.874287161624311 -2.6868984302083723 19.162406167006097 2 1 1.0016462505133576 0 0 0
|
||||
22 8 -4.466038023713098 -0.16009445500929992 14.199167217812603 2 1 1.0016462505133576 0 0 0
|
||||
23 1 -3.805032901797115 1.3047989425274054 9.939919176722297 2 1 1.0016462505133576 0 0 0
|
||||
24 2 -0.3645313828582167 2.0504253339486334 6.749830838323167 2 1 1.0016462505133576 0 0 0
|
||||
25 3 2.8696234661228 1.1843850873648512 3.5779840008575166 2 1 1.0016462505133576 0 0 0
|
||||
26 4 4.584052070339748 -2.4162961106383802 0.4178747538604132 2 1 1.0016462505133576 0 0 0
|
||||
|
||||
Velocities
|
||||
|
||||
1 -0.0007092826233374404 -0.0011683182237858898 0.0009345415878891811 -0.19711297351977997 0.3471662755040702 1.1876949496899232
|
||||
2 0.0001692806579311005 0.001454411904318072 -0.0009132068521112497 0.40085230919108755 -0.18887849087800404 0.047091827325408245
|
||||
3 0.00026721094548725233 -0.0018474107413693995 -7.33687581476124e-05 0.46267958346439353 1.0098887515959383 0.6393407481151142
|
||||
4 0.0005530692647148845 6.276724836348722e-05 0.0011760622369354724 0.485473149019376 -1.016731064060453 0.4763136256195711
|
||||
5 0.0010959077967915062 -0.002073578927849095 0.0009200279724368436 1.0623586979165884 1.065939836735458 -1.5037672467577814
|
||||
6 -0.0011992989214254961 -0.0008200232774176946 -1.878586889584186e-05 0.2637939462292815 0.9503989065450423 -1.6260870297579495
|
||||
7 0.0006177535901987009 0.000518919774167013 0.0003998839732602718 -0.6408171281169938 0.36348341926995353 -1.375803360797847
|
||||
8 0.00016059142531900045 -0.0006450606532728585 0.0008669204672450051 -0.7477778258878353 0.47361246994539824 -0.5810846842200627
|
||||
9 8.231216517048786e-05 6.015188190262039e-05 6.125792756154739e-05 -0.4607197796707098 0.5637456934375974 0.26087415190460156
|
||||
10 -0.000500147138046807 -0.000463066044342822 0.000355851169196805 -0.36328886676626787 -0.43369687106567045 0.5273136714151697
|
||||
11 0.0007757175683907118 -8.926233267161596e-05 -0.0008385947169209714 -0.4808110547195639 0.46086842856246785 -1.2339214306000716
|
||||
12 -0.001263650191118318 0.00028219137594863816 -0.0014126973797773772 0.3775783079049196 -0.1807429862945671 2.0452684483124046
|
||||
13 -3.2579866050976174e-05 0.0002635521160422669 0.0004611578260851882 -0.7261457161482728 -0.9102614938022983 -0.950223070000176
|
||||
14 -0.0004505866261683952 0.0009690259297353478 -0.0013620790360894626 0.7053189033188233 0.2384556381419323 0.771670025066328
|
||||
15 0.0011631309106043411 0.00044570587091719976 8.76640977124226e-05 0.6336939456886027 0.23680623944908769 0.16348552253269122
|
||||
16 -6.374073980270027e-05 -0.0002931008886831666 0.001121388312515121 -0.22078626344978855 0.4828157321900567 -1.5155692478249987
|
||||
17 -0.0010186027342478764 -0.002155869929612435 -0.0002602846290421834 -0.7045426361887308 -0.35130535920917716 -1.3344634305851248
|
||||
18 0.0013185658893551267 2.047723112341404e-05 -0.0005696586063762746 -1.6060222297755182 0.09031942024852611 0.9877781291576422
|
||||
19 -0.0014036986693625635 0.0012719382904391608 1.897600955961397e-05 0.9208051089916969 -1.6695360996503725 0.9680334678576618
|
||||
20 -0.0017040889747209288 0.00025337668854442876 -0.0001691840039087206 -0.5820811149791364 -0.6584676155867104 -0.13895286467266474
|
||||
21 -0.0012832301288169161 0.00023432762658239688 0.0004175391014650396 -0.368479743293301 -0.13070387294699928 -0.7972536298008709
|
||||
22 0.000425865764618422 0.0005323528439718917 -0.00037084207215630813 -1.987484231007066 -0.8187640783546725 0.8567029127863278
|
||||
23 -0.0004662057261624694 -0.0009522140435800978 0.0009625566807134454 0.07570418552326717 -1.5530387610102858 1.0623583182518839
|
||||
24 -0.0008020353772621954 0.0006130763545177365 0.000256600283460346 -0.4133480645752746 -1.123177366593782 0.34895664453469977
|
||||
25 -0.0007357778484794694 0.0004842720240985607 -0.0010361169830474496 0.23875324331203535 -0.5925750420871833 0.1484289925046781
|
||||
26 -0.000301663155222858 0.001775092432198598 -0.0009822913284976214 0.0628202961121918 0.11750852756815655 -0.8762490863383418
|
||||
|
||||
Bonds
|
||||
|
||||
1 1 1 2
|
||||
2 1 2 3
|
||||
3 1 3 4
|
||||
4 1 4 5
|
||||
5 1 5 6
|
||||
6 1 6 7
|
||||
7 1 7 8
|
||||
8 1 8 9
|
||||
9 1 9 10
|
||||
10 1 10 11
|
||||
11 1 11 12
|
||||
12 1 12 13
|
||||
13 1 14 15
|
||||
14 1 15 16
|
||||
15 1 16 17
|
||||
16 1 17 18
|
||||
17 1 18 19
|
||||
18 1 19 20
|
||||
19 1 20 21
|
||||
20 1 21 22
|
||||
21 1 22 23
|
||||
22 1 23 24
|
||||
23 1 24 25
|
||||
24 1 25 26
|
||||
|
||||
Ellipsoids
|
||||
|
||||
1 9.999999997766462 9.999999997766462 9.999999997766462 0.9970278940278272 0.0014876174054512252 0.0750547523448584 0.017319055267040844
|
||||
2 9.999999997766462 9.999999997766462 9.999999997766462 0.9059171712388804 0.007913225291438054 0.04634256838354512 0.42083705406683053
|
||||
3 9.999999997766462 9.999999997766462 9.999999997766462 0.7657426991864452 0.028071560533125216 0.13224385975981257 0.6287779160305484
|
||||
4 9.999999997766462 9.999999997766462 9.999999997766462 0.5238981696613685 0.0516703526741727 0.1609645534282743 0.8348360887142046
|
||||
5 9.999999997766462 9.999999997766462 9.999999997766462 0.30973290897949424 0.0750672191209306 0.23962885621884192 0.9170651279902646
|
||||
6 9.999999997766462 9.999999997766462 9.999999997766462 -0.050269263744563454 0.08142241031464711 0.09584085715741358 0.9907865170259763
|
||||
7 9.999999997766462 9.999999997766462 9.999999997766462 -0.3805122714271814 0.08965734720629535 0.057827749665601925 0.9186010683391725
|
||||
8 9.999999997766462 9.999999997766462 9.999999997766462 -0.6066322463100545 0.015286960797006149 0.035984536832974555 0.7940206166563465
|
||||
9 9.999999997766462 9.999999997766462 9.999999997766462 0.771660293819677 0.02607541526374929 -0.08047223278265907 -0.6303845520092687
|
||||
10 9.999999997766462 9.999999997766462 9.999999997766462 0.9119628434851113 0.03686258000931541 -0.11017000132786052 -0.3934812487336936
|
||||
11 9.999999997766462 9.999999997766462 9.999999997766462 0.9917294290821066 0.05835078551401739 -0.08073737536574405 -0.08092837290732445
|
||||
12 9.999999997766462 9.999999997766462 9.999999997766462 0.9763527785523285 0.06753089597617556 0.004847281702108697 0.205307899901351
|
||||
13 9.999999997766462 9.999999997766462 9.999999997766462 0.8553397145502984 0.1399133966151149 0.07233200118835512 0.49354462388392356
|
||||
14 9.999999997766462 9.999999997766462 9.999999997766462 0.014416326682630282 -0.533642571147991 0.8442695396252617 0.04718813669228716
|
||||
15 9.999999997766462 9.999999997766462 9.999999997766462 0.14095892784917538 -0.2201285495070387 0.9406003462562982 -0.21666792788520955
|
||||
16 9.999999997766462 9.999999997766462 9.999999997766462 0.07323967796304806 0.05035907488974361 0.963136526452943 -0.2539053850556888
|
||||
17 9.999999997766462 9.999999997766462 9.999999997766462 0.030254986187638885 0.39195467212588947 0.9164794947567249 -0.07430684019611289
|
||||
18 9.999999997766462 9.999999997766462 9.999999997766462 -0.03080283760241768 0.6526511470205414 0.7481495879677094 -0.11562810865943304
|
||||
19 9.999999997766462 9.999999997766462 9.999999997766462 -0.09450197979153381 0.7469150592813072 0.6556128255138505 -0.0579576833217777
|
||||
20 9.999999997766462 9.999999997766462 9.999999997766462 -0.12903334341475137 0.9222523214328698 0.3501336268694509 -0.10103214950765672
|
||||
21 9.999999997766462 9.999999997766462 9.999999997766462 -0.0069954457806870336 0.9888131084284681 -0.09413955816471489 -0.11548785185859346
|
||||
22 9.999999997766462 9.999999997766462 9.999999997766462 0.029336230851923526 0.9805894852440379 -0.19236800606724952 -0.02404573205262194
|
||||
23 9.999999997766462 9.999999997766462 9.999999997766462 0.03080980270092377 0.872234086776475 -0.4869211139732921 0.03415088124407873
|
||||
24 9.999999997766462 9.999999997766462 9.999999997766462 0.007237815450514786 0.690265186998662 -0.7210993183911308 0.05913847022922672
|
||||
25 9.999999997766462 9.999999997766462 9.999999997766462 0.06694683426684143 -0.46894411325316443 0.8712038661029582 -0.12889283810247346
|
||||
26 9.999999997766462 9.999999997766462 9.999999997766462 0.07581973147109407 -0.10215114654759445 0.9759556607577902 -0.17699451916228467
|
||||
@ -0,0 +1,828 @@
|
||||
#!/usr/bin/env python
|
||||
"""
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
https://www.lammps.org/ Sandia National Laboratories
|
||||
LAMMPS Development team: developers@lammps.org
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
Contributing author: Oliver Henrich (University of Strathclyde, Glasgow)
|
||||
------------------------------------------------------------------------- */
|
||||
"""
|
||||
"""
|
||||
Creates unique base-pairings to avoid asymmetrical H-bonds.
|
||||
|
||||
Modified to create the bead wall setup.
|
||||
N_BEADS is the number of beads along one direction, the final system will have N_BEADS^2 beads in the wall. N_BEADS should be set to be odd number.
|
||||
"""
|
||||
|
||||
|
||||
#Define number of base-pairs per turn for B-form DNA
|
||||
N = 10.5
|
||||
#Define distance between the big bead and the centre of mass of the last base-pair
|
||||
BEAD_OFFSET = 2.0
|
||||
WALL_PARTICLE_SIZE = 2.0
|
||||
N_BEADS = 11
|
||||
|
||||
#Number of unique base type groups (1-4) ACGT counts as one group
|
||||
N_BASE_TYPES = 20
|
||||
|
||||
|
||||
"""
|
||||
Import basic modules
|
||||
"""
|
||||
import sys, os, timeit
|
||||
|
||||
from timeit import default_timer as timer
|
||||
start_time = timer()
|
||||
"""
|
||||
Try to import numpy; if failed, import a local version mynumpy
|
||||
which needs to be provided
|
||||
"""
|
||||
try:
|
||||
import numpy as np
|
||||
except:
|
||||
print("numpy not found. Exiting.", file=sys.stderr)
|
||||
sys.exit(1)
|
||||
|
||||
"""
|
||||
Check that the required arguments (box offset and size in simulation units
|
||||
and the sequence file were provided
|
||||
"""
|
||||
try:
|
||||
box_offset = float(sys.argv[1])
|
||||
box_length = float(sys.argv[2])
|
||||
infile = sys.argv[3]
|
||||
if len(sys.argv) == 4:
|
||||
topo = 'strand'
|
||||
lk = 0
|
||||
elif len(sys.argv) == 5:
|
||||
topo = 'strand'
|
||||
lk = int(sys.argv[4])
|
||||
|
||||
except:
|
||||
print("Usage: %s <%s> <%s> <%s> <%s> " % (sys.argv[0], \
|
||||
"box offset", "box length", "file with sequences", "[Lk]"), file=sys.stderr)
|
||||
sys.exit(1)
|
||||
box = np.array ([box_length, box_length, box_length])
|
||||
|
||||
"""
|
||||
Try to open the file and fail gracefully if file cannot be opened
|
||||
"""
|
||||
try:
|
||||
inp = open (infile, 'r')
|
||||
inp.close()
|
||||
except:
|
||||
print("Could not open file '%s' for reading. \
|
||||
Aborting." % infile, file=sys.stderr)
|
||||
sys.exit(2)
|
||||
|
||||
# return parts of a string
|
||||
def partition(s, d):
|
||||
if d in s:
|
||||
sp = s.split(d, 1)
|
||||
return sp[0], d, sp[1]
|
||||
else:
|
||||
return s, "", ""
|
||||
|
||||
"""
|
||||
Define the model constants
|
||||
"""
|
||||
# set model constants
|
||||
PI = np.pi
|
||||
POS_BASE = 0.4
|
||||
POS_BACK = -0.4
|
||||
EXCL_RC1 = 0.711879214356
|
||||
EXCL_RC2 = 0.335388426126
|
||||
EXCL_RC3 = 0.52329943261
|
||||
|
||||
"""
|
||||
Define auxiliary variables for the construction of a helix
|
||||
"""
|
||||
# center of the double strand
|
||||
COM_CENTRE_DS = POS_BASE + 0.2
|
||||
|
||||
# ideal rise between two consecutive nucleotides on the
|
||||
# same strand which are to be base paired in a duplex
|
||||
BASE_BASE = 0.3897628551303122
|
||||
|
||||
# cutoff distance for overlap check
|
||||
RC2 = 16
|
||||
|
||||
# squares of the excluded volume distances for overlap check
|
||||
RC2_BACK = EXCL_RC1**2
|
||||
RC2_BASE = EXCL_RC2**2
|
||||
RC2_BACK_BASE = EXCL_RC3**2
|
||||
|
||||
# enumeration to translate from letters to numbers and vice versa
|
||||
number_to_base = {1 : 'A', 2 : 'C', 3 : 'G', 4 : 'T'}
|
||||
base_to_number = {'A' : 1, 'a' : 1, 'C' : 2, 'c' : 2,
|
||||
'G' : 3, 'g' : 3, 'T' : 4, 't' : 4}
|
||||
|
||||
# auxiliary arrays
|
||||
positions = []
|
||||
a1s = []
|
||||
a3s = []
|
||||
quaternions = []
|
||||
|
||||
newpositions = []
|
||||
newa1s = []
|
||||
newa3s = []
|
||||
|
||||
basetype = []
|
||||
strandnum = []
|
||||
|
||||
bonds = []
|
||||
|
||||
"""
|
||||
Convert local body frame to quaternion DOF
|
||||
"""
|
||||
def exyz_to_quat (mya1, mya3):
|
||||
|
||||
mya2 = np.cross(mya3, mya1)
|
||||
myquat = [1,0,0,0]
|
||||
|
||||
q0sq = 0.25 * (mya1[0] + mya2[1] + mya3[2] + 1.0)
|
||||
q1sq = q0sq - 0.5 * (mya2[1] + mya3[2])
|
||||
q2sq = q0sq - 0.5 * (mya1[0] + mya3[2])
|
||||
q3sq = q0sq - 0.5 * (mya1[0] + mya2[1])
|
||||
|
||||
# some component must be greater than 1/4 since they sum to 1
|
||||
# compute other components from it
|
||||
|
||||
if q0sq >= 0.25:
|
||||
myquat[0] = np.sqrt(q0sq)
|
||||
myquat[1] = (mya2[2] - mya3[1]) / (4.0*myquat[0])
|
||||
myquat[2] = (mya3[0] - mya1[2]) / (4.0*myquat[0])
|
||||
myquat[3] = (mya1[1] - mya2[0]) / (4.0*myquat[0])
|
||||
elif q1sq >= 0.25:
|
||||
myquat[1] = np.sqrt(q1sq)
|
||||
myquat[0] = (mya2[2] - mya3[1]) / (4.0*myquat[1])
|
||||
myquat[2] = (mya2[0] + mya1[1]) / (4.0*myquat[1])
|
||||
myquat[3] = (mya1[2] + mya3[0]) / (4.0*myquat[1])
|
||||
elif q2sq >= 0.25:
|
||||
myquat[2] = np.sqrt(q2sq)
|
||||
myquat[0] = (mya3[0] - mya1[2]) / (4.0*myquat[2])
|
||||
myquat[1] = (mya2[0] + mya1[1]) / (4.0*myquat[2])
|
||||
myquat[3] = (mya3[1] + mya2[2]) / (4.0*myquat[2])
|
||||
elif q3sq >= 0.25:
|
||||
myquat[3] = np.sqrt(q3sq)
|
||||
myquat[0] = (mya1[1] - mya2[0]) / (4.0*myquat[3])
|
||||
myquat[1] = (mya3[0] + mya1[2]) / (4.0*myquat[3])
|
||||
myquat[2] = (mya3[1] + mya2[2]) / (4.0*myquat[3])
|
||||
|
||||
norm = 1.0/np.sqrt(myquat[0]*myquat[0] + myquat[1]*myquat[1] + \
|
||||
myquat[2]*myquat[2] + myquat[3]*myquat[3])
|
||||
myquat[0] *= norm
|
||||
myquat[1] *= norm
|
||||
myquat[2] *= norm
|
||||
myquat[3] *= norm
|
||||
|
||||
return np.array([myquat[0],myquat[1],myquat[2],myquat[3]])
|
||||
|
||||
"""
|
||||
Adds a strand to the system by appending it to the array of previous strands
|
||||
"""
|
||||
def add_strands (mynewpositions, mynewa1s, mynewa3s):
|
||||
overlap = False
|
||||
|
||||
# This is a simple check for each of the particles where for previously
|
||||
# placed particles i we check whether it overlaps with any of the
|
||||
# newly created particles j
|
||||
|
||||
print("## Checking for overlaps", file=sys.stdout)
|
||||
|
||||
for i in range(len(positions)):
|
||||
|
||||
p = positions[i]
|
||||
pa1 = a1s[i]
|
||||
|
||||
for j in range (len(mynewpositions)):
|
||||
|
||||
q = mynewpositions[j]
|
||||
qa1 = mynewa1s[j]
|
||||
|
||||
# skip particles that are anyway too far away
|
||||
dr = p - q
|
||||
dr -= box * np.rint (dr / box)
|
||||
if np.dot(dr, dr) > RC2:
|
||||
continue
|
||||
|
||||
# base site and backbone site of the two particles
|
||||
p_pos_back = p + pa1 * POS_BACK
|
||||
p_pos_base = p + pa1 * POS_BASE
|
||||
q_pos_back = q + qa1 * POS_BACK
|
||||
q_pos_base = q + qa1 * POS_BASE
|
||||
|
||||
# check for no overlap between the two backbone sites
|
||||
dr = p_pos_back - q_pos_back
|
||||
dr -= box * np.rint (dr / box)
|
||||
if np.dot(dr, dr) < RC2_BACK:
|
||||
overlap = True
|
||||
|
||||
# check for no overlap between the two base sites
|
||||
dr = p_pos_base - q_pos_base
|
||||
dr -= box * np.rint (dr / box)
|
||||
if np.dot(dr, dr) < RC2_BASE:
|
||||
overlap = True
|
||||
|
||||
# check for no overlap between backbone site of particle p
|
||||
# with base site of particle q
|
||||
dr = p_pos_back - q_pos_base
|
||||
dr -= box * np.rint (dr / box)
|
||||
if np.dot(dr, dr) < RC2_BACK_BASE:
|
||||
overlap = True
|
||||
|
||||
# check for no overlap between base site of particle p and
|
||||
# backbone site of particle q
|
||||
dr = p_pos_base - q_pos_back
|
||||
dr -= box * np.rint (dr / box)
|
||||
if np.dot(dr, dr) < RC2_BACK_BASE:
|
||||
overlap = True
|
||||
|
||||
# exit if there is an overlap
|
||||
if overlap:
|
||||
return False
|
||||
|
||||
# append to the existing list if no overlap is found
|
||||
if not overlap:
|
||||
|
||||
for p in mynewpositions:
|
||||
positions.append(p)
|
||||
for p in mynewa1s:
|
||||
a1s.append (p)
|
||||
for p in mynewa3s:
|
||||
a3s.append (p)
|
||||
# calculate quaternion from local body frame and append
|
||||
for ia in range(len(mynewpositions)):
|
||||
mynewquaternions = exyz_to_quat(mynewa1s[ia],mynewa3s[ia])
|
||||
quaternions.append(mynewquaternions)
|
||||
|
||||
return True
|
||||
|
||||
"""
|
||||
Calculate angle of rotation site to site
|
||||
"""
|
||||
def get_angle(bp):
|
||||
#n, minimal number of bases per turn
|
||||
n = 10.5
|
||||
found = False
|
||||
while found == False:
|
||||
turns = bp/n
|
||||
diff = abs( turns - round(turns))
|
||||
if diff < 0.03:
|
||||
found = True
|
||||
turns = round(turns)+lk
|
||||
angle = (360*turns)/bp
|
||||
angle = round (angle,2)
|
||||
#angle =round( 360/n,2)
|
||||
elif n > 11.5:
|
||||
angle = 35.9
|
||||
found = True
|
||||
else:
|
||||
n += 0.02
|
||||
return angle
|
||||
|
||||
|
||||
def get_angle2(bp):
|
||||
turns = bp/N + lk
|
||||
angle = (360*turns)/bp
|
||||
|
||||
return angle
|
||||
|
||||
|
||||
|
||||
"""
|
||||
Returns the rotation matrix defined by an axis and angle
|
||||
"""
|
||||
def get_rotation_matrix(axis, anglest, nbp=0):
|
||||
# The argument anglest can be either an angle in radiants
|
||||
# (accepted types are float, int or np.float64 or np.float64)
|
||||
# or a tuple [angle, units] where angle is a number and
|
||||
# units is a string. It tells the routine whether to use degrees,
|
||||
# radiants (the default) or base pairs turns.
|
||||
if not isinstance (anglest, (np.float64, np.float32, float, int)):
|
||||
if len(anglest) > 1:
|
||||
if anglest[1] in ["degrees", "deg", "o"]:
|
||||
angle = (np.pi / 180.) * (anglest[0])
|
||||
elif anglest[1] in ["bp"]:
|
||||
if nbp == 0:
|
||||
angle = int(anglest[0]) * (np.pi / 180.) * (35.9)
|
||||
else:
|
||||
ang = get_angle2(nbp)
|
||||
angle = int(anglest[0]) * (np.pi / 180.) * (ang)
|
||||
else:
|
||||
angle = float(anglest[0])
|
||||
else:
|
||||
angle = float(anglest[0])
|
||||
else:
|
||||
angle = float(anglest) # in degrees (?)
|
||||
|
||||
axis = np.array(axis)
|
||||
axis /= np.sqrt(np.dot(axis, axis))
|
||||
|
||||
ct = np.cos(angle)
|
||||
st = np.sin(angle)
|
||||
olc = 1. - ct
|
||||
x, y, z = axis
|
||||
|
||||
return np.array([[olc*x*x+ct, olc*x*y-st*z, olc*x*z+st*y],
|
||||
[olc*x*y+st*z, olc*y*y+ct, olc*y*z-st*x],
|
||||
[olc*x*z-st*y, olc*y*z+st*x, olc*z*z+ct]])
|
||||
|
||||
"""
|
||||
Generates the position and orientation vectors of a
|
||||
(single or double) strand from a sequence string
|
||||
"""
|
||||
def generate_strand(bp, sequence=None, start_pos=np.array([0, 0, 0]), \
|
||||
dir=np.array([0, 0, 1]), perp=False, double=True, rot=0.):
|
||||
# generate empty arrays
|
||||
mynewpositions, mynewa1s, mynewa3s = [], [], []
|
||||
|
||||
# cast the provided start_pos array into a numpy array
|
||||
start_pos = np.array(start_pos, dtype=float)
|
||||
|
||||
# overall direction of the helix
|
||||
dir = np.array(dir, dtype=float)
|
||||
#if sequence == None:
|
||||
# sequence = np.random.randint(1, 5, bp)
|
||||
|
||||
# the elseif here is most likely redundant
|
||||
#elif len(sequence) != bp:
|
||||
# n = bp - len(sequence)
|
||||
# sequence += np.random.randint(1, 5, n)
|
||||
# print("sequence is too short, adding %d random bases" % n, file=sys.stderr)
|
||||
|
||||
# normalize direction
|
||||
dir_norm = np.sqrt(np.dot(dir,dir))
|
||||
if dir_norm < 1e-10:
|
||||
print("direction must be a valid vector,\
|
||||
defaulting to (0, 0, 1)", file=sys.stderr)
|
||||
dir = np.array([0, 0, 1])
|
||||
else: dir /= dir_norm
|
||||
|
||||
# find a vector orthogonal to dir to act as helix direction,
|
||||
# if not provided switch off random orientation
|
||||
if perp is None or perp is False:
|
||||
v1 = np.random.random_sample(3)
|
||||
# comment in to suppress randomized base vector
|
||||
v1 = [1,0,0]
|
||||
v1 -= dir * (np.dot(dir, v1))
|
||||
v1 /= np.sqrt(sum(v1*v1))
|
||||
else:
|
||||
v1 = perp;
|
||||
|
||||
# generate rotational matrix representing the overall rotation of the helix
|
||||
R0 = get_rotation_matrix(dir, rot)
|
||||
|
||||
# rotation matrix corresponding to one step along the helix
|
||||
R = get_rotation_matrix(dir, [1, "bp"],bp)
|
||||
|
||||
# set the vector a1 (backbone to base) to v1
|
||||
a1 = v1
|
||||
|
||||
# apply the global rotation to a1
|
||||
a1 = np.dot(R0, a1)
|
||||
|
||||
# set the position of the fist backbone site to start_pos
|
||||
rb = np.array(start_pos)
|
||||
|
||||
# set a3 to the direction of the helix
|
||||
a3 = dir
|
||||
|
||||
for i in range(bp):
|
||||
# work out the position of the centre of mass of the nucleotide
|
||||
rcom = rb - COM_CENTRE_DS * a1
|
||||
|
||||
# append to newpositions
|
||||
mynewpositions.append(rcom)
|
||||
mynewa1s.append(a1)
|
||||
mynewa3s.append(a3)
|
||||
|
||||
# if we are not at the end of the helix, we work out a1 and rb for the
|
||||
# next nucleotide along the helix
|
||||
if i != bp - 1:
|
||||
a1 = np.dot(R, a1)
|
||||
rb += a3 * BASE_BASE
|
||||
|
||||
# if we are working on a double strand, we do a cycle similar
|
||||
# to the previous one but backwards
|
||||
if double == True:
|
||||
a1 = -a1
|
||||
a3 = -dir
|
||||
R = R.transpose()
|
||||
for i in range(bp):
|
||||
rcom = rb - COM_CENTRE_DS * a1
|
||||
mynewpositions.append (rcom)
|
||||
mynewa1s.append (a1)
|
||||
mynewa3s.append (a3)
|
||||
a1 = np.dot(R, a1)
|
||||
rb += a3 * BASE_BASE
|
||||
|
||||
|
||||
#Calculate the positions of the bead wall
|
||||
|
||||
last_base1 = mynewpositions[int( len(mynewpositions)/2 - 1) ]
|
||||
last_base2 = mynewpositions[int( len(mynewpositions)/2) ]
|
||||
mid_point = (last_base1 + last_base2) / 2
|
||||
|
||||
NN = N_BEADS**2
|
||||
p1 = [mid_point[0] - (N_BEADS-1)*WALL_PARTICLE_SIZE, mid_point[1] - (N_BEADS-1)*WALL_PARTICLE_SIZE, mid_point[2] + BEAD_OFFSET ]
|
||||
for i in range(N_BEADS):
|
||||
for j in range(N_BEADS):
|
||||
position = [ p1[0] + 2*i*WALL_PARTICLE_SIZE, p1[1] + 2*j*WALL_PARTICLE_SIZE, p1[2]]
|
||||
mynewa1s.append([1,0,0])
|
||||
mynewa3s.append([1,0,0])
|
||||
mynewpositions.append(position)
|
||||
|
||||
assert (len (mynewpositions) > 0)
|
||||
|
||||
return [mynewpositions, mynewa1s, mynewa3s]
|
||||
|
||||
|
||||
|
||||
"""
|
||||
Main function for this script.
|
||||
Reads a text file with the following format:
|
||||
- Each line contains the sequence for a single strand (A,C,G,T)
|
||||
- Lines beginning with the keyword 'DOUBLE' produce double-stranded DNA
|
||||
|
||||
Ex: Two ssDNA (single stranded DNA)
|
||||
ATATATA
|
||||
GCGCGCG
|
||||
|
||||
Ex: Two strands, one double stranded, the other single stranded.
|
||||
DOUBLE AGGGCT
|
||||
CCTGTA
|
||||
|
||||
"""
|
||||
|
||||
def read_strands(filename):
|
||||
try:
|
||||
infile = open (filename)
|
||||
except:
|
||||
print("Could not open file '%s'. Aborting." % filename, file=sys.stderr)
|
||||
sys.exit(2)
|
||||
|
||||
# This block works out the number of nucleotides and strands by reading
|
||||
# the number of non-empty lines in the input file and the number of letters,
|
||||
# taking the possible DOUBLE keyword into account.
|
||||
nstrands, nnucl, nbonds = 0, 0, 0
|
||||
lines = infile.readlines()
|
||||
for line in lines:
|
||||
line = line.upper().strip()
|
||||
if len(line) == 0:
|
||||
continue
|
||||
if line[:6] == 'DOUBLE':
|
||||
line = line.split()[1]
|
||||
length = len(line)
|
||||
print("## Found duplex of %i base pairs" % length, file=sys.stdout)
|
||||
nnucl += 2*length
|
||||
nstrands += 2
|
||||
nbonds+= 2*length
|
||||
|
||||
else:
|
||||
line = line.split()[0]
|
||||
length = len(line)
|
||||
print("## Found single strand of %i bases" % length, file=sys.stdout)
|
||||
nnucl += length
|
||||
nstrands += 1
|
||||
if topo == 'ring':
|
||||
nbonds =+ length
|
||||
else:
|
||||
nbonds += length+1
|
||||
# rewind the sequence input file
|
||||
infile.seek(0)
|
||||
|
||||
print("## nstrands, nnucl = ", nstrands, nnucl, file=sys.stdout)
|
||||
|
||||
# generate the data file in LAMMPS format
|
||||
try:
|
||||
out = open ("data.oxdna", "w")
|
||||
except:
|
||||
print("Could not open data file for writing. Aborting.", file=sys.stderr)
|
||||
sys.exit(2)
|
||||
|
||||
lines = infile.readlines()
|
||||
nlines = len(lines)
|
||||
i = 1
|
||||
myns = 0
|
||||
noffset = 1
|
||||
|
||||
for line in lines:
|
||||
line = line.upper().strip()
|
||||
|
||||
# skip empty lines
|
||||
if len(line) == 0:
|
||||
i += 1
|
||||
continue
|
||||
|
||||
# block for duplexes: last argument of the generate function
|
||||
# is set to 'True'
|
||||
if line[:6] == 'DOUBLE':
|
||||
line = line.split()[1]
|
||||
length = len(line)
|
||||
seq = [(base_to_number[x]) for x in line]
|
||||
seq = np.array(seq,dtype=int)
|
||||
n_a, n_c, n_g, n_t = 0, 0, 0, 0
|
||||
for s in range(seq.size):
|
||||
if seq[s] == 1:
|
||||
n_a += 1
|
||||
elif seq[s] == 2:
|
||||
n_c += 1
|
||||
elif seq[s] ==3:
|
||||
n_g += 1
|
||||
elif seq[s] == 4:
|
||||
n_t += 1
|
||||
smallest_n_bases = n_c
|
||||
if n_a < n_c:
|
||||
smallest_n_bases = n_a
|
||||
if smallest_n_bases > n_t:
|
||||
smallest_n_bases = n_t
|
||||
if smallest_n_bases > n_g:
|
||||
smallest_n_bases = n_g
|
||||
|
||||
if smallest_n_bases < N_BASE_TYPES:
|
||||
print('## Not enough occurrences of base types in the sequence for ' + str(N_BASE_TYPES))
|
||||
print('## unique base types, switching to ' + str(smallest_n_bases) + ' unique types')
|
||||
else:
|
||||
smallest_n_bases = N_BASE_TYPES
|
||||
|
||||
a, c, g, t = -3, -2, -1, 0
|
||||
for s in range(seq.size):
|
||||
if seq[s] == 1:
|
||||
if a < (smallest_n_bases*4-3):
|
||||
a += 4
|
||||
else:
|
||||
a = 1
|
||||
seq[s] = a
|
||||
|
||||
elif seq[s] == 2:
|
||||
if c < (smallest_n_bases*4-2):
|
||||
c += 4
|
||||
else:
|
||||
c = 2
|
||||
seq[s] = c
|
||||
|
||||
elif seq[s] == 3:
|
||||
if g < (smallest_n_bases*4-1):
|
||||
g += 4
|
||||
else:
|
||||
g = 3
|
||||
seq[s] = g
|
||||
elif seq[s] == 4:
|
||||
if t < (smallest_n_bases*4):
|
||||
t += 4
|
||||
else:
|
||||
t = 4
|
||||
seq[s] = t
|
||||
|
||||
|
||||
|
||||
myns += 1
|
||||
|
||||
for b in range(length):
|
||||
basetype.append(seq[b])
|
||||
strandnum.append(myns)
|
||||
|
||||
for b in range(length-1):
|
||||
bondpair = [noffset + b, noffset + b + 1]
|
||||
bonds.append(bondpair)
|
||||
|
||||
|
||||
noffset += length
|
||||
|
||||
# create the sequence of the second strand as made of
|
||||
# complementary bases
|
||||
#seq2 = [5-s for s in seq]
|
||||
seq2 = seq
|
||||
for s in range(seq2.size):
|
||||
if seq2[s]%4 == 1:
|
||||
seq2[s] += 3
|
||||
elif seq2[s]%4 == 2:
|
||||
seq2[s] += 1
|
||||
elif seq2[s]%4 == 3:
|
||||
seq2[s] -= 1
|
||||
elif seq2[s]%4 == 0:
|
||||
seq2[s] -= 3
|
||||
|
||||
#seq2.reverse()
|
||||
|
||||
myns += 1
|
||||
|
||||
for b in range(length):
|
||||
basetype.append(seq2[b])
|
||||
strandnum.append(myns)
|
||||
|
||||
for b in range(length-1):
|
||||
bondpair = [noffset + b, noffset + b + 1]
|
||||
bonds.append(bondpair)
|
||||
|
||||
|
||||
#create wall bead types
|
||||
bead_type = 4*smallest_n_bases + 1
|
||||
for i in range(N_BEADS**2):
|
||||
|
||||
basetype.append(bead_type)
|
||||
basetype.append(bead_type)
|
||||
strandnum.append(bead_type)
|
||||
strandnum.append(bead_type)
|
||||
#bonds.append([length, noffset + length])
|
||||
#bonds.append([length+1, noffset + length])
|
||||
|
||||
noffset += length
|
||||
|
||||
print("## Created duplex of %i bases" % (2*length), file=sys.stdout)
|
||||
|
||||
# generate random position of the first nucleotide
|
||||
com = box_offset + np.random.random_sample(3) * box
|
||||
# comment out to randomize
|
||||
com = [0,0,0]
|
||||
|
||||
# generate the random direction of the helix
|
||||
axis = np.random.random_sample(3)
|
||||
# comment out to randomize
|
||||
axis = [0,0,1]
|
||||
axis /= np.sqrt(np.dot(axis, axis))
|
||||
|
||||
# use the generate function defined above to create
|
||||
# the position and orientation vector of the strand
|
||||
if topo == 'ring':
|
||||
newpositions, newa1s, newa3s = generate_ring(len(line), \
|
||||
sequence=seq, dir=axis, start_pos=com, double=True)
|
||||
else:
|
||||
newpositions, newa1s, newa3s = generate_strand(len(line), \
|
||||
sequence=seq, dir=axis, start_pos=com, double=True)
|
||||
|
||||
# generate a new position for the strand until it does not overlap
|
||||
# with anything already present
|
||||
start = timer()
|
||||
while not add_strands(newpositions, newa1s, newa3s):
|
||||
com = box_offset + np.random.random_sample(3) * box
|
||||
axis = np.random.random_sample(3)
|
||||
axis /= np.sqrt(np.dot(axis, axis))
|
||||
if topo == 'ring':
|
||||
newpositions, newa1s, newa3s = generate_ring(len(line), \
|
||||
sequence=seq, dir=axis, start_pos=com, double=True)
|
||||
else:
|
||||
newpositions, newa1s, newa3s = generate_strand(len(line), \
|
||||
sequence=seq, dir=axis, start_pos=com, double=True)
|
||||
print("## Trying %i" % i, file=sys.stdout)
|
||||
end = timer()
|
||||
print("## Added duplex of %i bases (line %i/%i) in %.2fs, now at %i/%i" % \
|
||||
(2*length, i, nlines, end-start, len(positions), nnucl), file=sys.stdout)
|
||||
|
||||
# block for single strands: last argument of the generate function
|
||||
# is set to 'False'
|
||||
else:
|
||||
length = len(line)
|
||||
seq = [(base_to_number[x]) for x in line]
|
||||
|
||||
myns += 1
|
||||
for b in range(length):
|
||||
basetype.append(seq[b])
|
||||
strandnum.append(myns)
|
||||
|
||||
for b in range(length-1):
|
||||
bondpair = [noffset + b, noffset + b + 1]
|
||||
bonds.append(bondpair)
|
||||
if topo == 'ring':
|
||||
bondpair = [noffset, noffset + length-1]
|
||||
bonds.append(bondpair)
|
||||
noffset += length
|
||||
|
||||
|
||||
# generate random position of the first nucleotide
|
||||
com = box_offset + np.random.random_sample(3) * box
|
||||
# comment out to randomize
|
||||
com = [-30,0,0]
|
||||
|
||||
# generate the random direction of the helix
|
||||
axis = np.random.random_sample(3)
|
||||
# comment out to randomize
|
||||
axis = [0,0,1]
|
||||
axis /= np.sqrt(np.dot(axis, axis))
|
||||
|
||||
print("## Created single strand of %i bases" % length, file=sys.stdout)
|
||||
if topo == 'ring':
|
||||
newpositions, newa1s, newa3s = generate_ring(length, \
|
||||
sequence=seq, dir=axis, start_pos=com, double=False)
|
||||
else:
|
||||
newpositions, newa1s, newa3s = generate_strand(length, \
|
||||
sequence=seq, dir=axis, start_pos=com, double=False)
|
||||
start = timer()
|
||||
while not add_strands(newpositions, newa1s, newa3s):
|
||||
com = box_offset + np.random.random_sample(3) * box
|
||||
axis = np.random.random_sample(3)
|
||||
axis /= np.sqrt(np.dot(axis, axis))
|
||||
if topo == 'ring':
|
||||
newpositions, newa1s, newa3s = generate_ring(length, \
|
||||
sequence=seq, dir=axis, start_pos=com, double=False)
|
||||
|
||||
else:
|
||||
newpositions, newa1s, newa3s = generate_strand(length, \
|
||||
sequence=seq, dir=axis, start_pos=com, double=False)
|
||||
print("## Trying %i" % (i), file=sys.stdout)
|
||||
end = timer()
|
||||
print("## Added single strand of %i bases (line %i/%i) in %.2fs, now at %i/%i" % \
|
||||
(length, i, nlines, end-start,len(positions), nnucl), file=sys.stdout)
|
||||
|
||||
i += 1
|
||||
|
||||
# sanity check
|
||||
#if not len(positions) == nnucl:
|
||||
# print(len(positions), nnucl)
|
||||
# raise AssertionError
|
||||
nnucl = nnucl + (N_BEADS**2)
|
||||
nbonds -= 4
|
||||
|
||||
out.write('# LAMMPS data file\n')
|
||||
out.write('%d atoms\n' % nnucl)
|
||||
out.write('%d ellipsoids\n' % nnucl)
|
||||
out.write('%d bonds\n' % nbonds)
|
||||
out.write('\n')
|
||||
out.write('%d atom types\n' %bead_type )
|
||||
out.write('1 bond types\n')
|
||||
out.write('\n')
|
||||
out.write('# System size\n')
|
||||
out.write('%f %f xlo xhi\n' % (box_offset,box_offset+box_length))
|
||||
out.write('%f %f ylo yhi\n' % (box_offset,box_offset+box_length))
|
||||
out.write('%f %f zlo zhi\n' % (0,box_length))
|
||||
|
||||
#out.write('\n')
|
||||
#out.write('Masses\n')
|
||||
#out.write('\n')
|
||||
#out.write('1 3.1575\n')
|
||||
#out.write('2 3.1575\n')
|
||||
#out.write('3 3.1575\n')
|
||||
#out.write('4 3.1575\n')
|
||||
#out.write('5 3.1575\n')
|
||||
|
||||
# for each nucleotide print a line under the headers
|
||||
# Atoms, Velocities, Ellipsoids and Bonds
|
||||
out.write('\n')
|
||||
out.write(\
|
||||
'# Atom-ID, type, position, molecule-ID, ellipsoid flag, density\n')
|
||||
out.write('Atoms\n')
|
||||
out.write('\n')
|
||||
|
||||
for i in range(nnucl):
|
||||
out.write('%d %d %22.15le %22.15le %22.15le %d 1 1\n' \
|
||||
% (i+1, basetype[i], \
|
||||
positions[i][0], positions[i][1], positions[i][2], \
|
||||
strandnum[i]))
|
||||
|
||||
out.write('\n')
|
||||
out.write('# Atom-ID, translational, rotational velocity\n')
|
||||
out.write('Velocities\n')
|
||||
out.write('\n')
|
||||
|
||||
for i in range(nnucl):
|
||||
out.write("%d %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le\n" \
|
||||
% (i+1,0.0,0.0,0.0,0.0,0.0,0.0))
|
||||
|
||||
out.write('\n')
|
||||
out.write('# Atom-ID, shape, quaternion\n')
|
||||
out.write('Ellipsoids\n')
|
||||
out.write('\n')
|
||||
|
||||
for i in range(nnucl):
|
||||
out.write(\
|
||||
"%d %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le\n" \
|
||||
% (i+1,1.1739845031423408,1.1739845031423408,1.1739845031423408, \
|
||||
quaternions[i][0],quaternions[i][1], quaternions[i][2],quaternions[i][3]))
|
||||
|
||||
out.write('\n')
|
||||
out.write('# Bond topology\n')
|
||||
out.write('Bonds\n')
|
||||
out.write('\n')
|
||||
|
||||
for i in range(nbonds):
|
||||
if i < nbonds-2:
|
||||
out.write("%d %d %d %d\n" % (i+1,1,bonds[i][0],bonds[i][1]))
|
||||
#else:
|
||||
|
||||
#out.write("%d %d %d %d\n" % (i+1,2,bonds[i][0],bonds[i][1]))
|
||||
|
||||
out.close()
|
||||
|
||||
print("## Wrote data to 'data.oxdna'", file=sys.stdout)
|
||||
print("## DONE", file=sys.stdout)
|
||||
|
||||
# call the above main() function, which executes the program
|
||||
read_strands (infile)
|
||||
|
||||
end_time=timer()
|
||||
runtime = end_time-start_time
|
||||
hours = runtime/3600
|
||||
minutes = (runtime-np.rint(hours)*3600)/60
|
||||
seconds = (runtime-np.rint(hours)*3600-np.rint(minutes)*60)%60
|
||||
print("## Total runtime %ih:%im:%.2fs" % (hours,minutes,seconds), file=sys.stdout)
|
||||
@ -0,0 +1,87 @@
|
||||
variable number equal 4
|
||||
variable ofreq equal 1000
|
||||
variable efreq equal 1000
|
||||
|
||||
variable ntype equal 4
|
||||
|
||||
variable T equal 300.0
|
||||
variable rhos equal 0.2
|
||||
|
||||
units real
|
||||
|
||||
dimension 3
|
||||
|
||||
newton on
|
||||
|
||||
boundary p p p
|
||||
|
||||
atom_style hybrid bond ellipsoid oxdna
|
||||
atom_modify sort 0 8.518
|
||||
|
||||
# Pair interactions require lists of neighbours to be calculated
|
||||
neighbor 17.036 bin
|
||||
neigh_modify every 10 delay 0 check yes
|
||||
|
||||
read_data data.duplex4.4type
|
||||
|
||||
mass * 315.8376 # sets per-type mass if not in data file
|
||||
set atom * mass 315.8376 # sets per-atom mass
|
||||
|
||||
group all type 1 4
|
||||
|
||||
# oxDNA2 bond interactions - FENE backbone
|
||||
bond_style oxdna2/fene
|
||||
bond_coeff * 11.92337812042065 2.1295 6.4430152
|
||||
special_bonds lj 0 1 1
|
||||
|
||||
# oxDNA pair interactions
|
||||
pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
|
||||
pair_coeff * * oxdna2/excv 11.92337812042065 5.9626 5.74965 11.92337812042065 4.38677 4.259 11.92337812042065 2.81094 2.72576
|
||||
pair_coeff * * oxdna2/stk seqdep ${T} 8.06199211612242 0.005309213 0.70439070204273 3.4072 7.6662 2.72576 6.3885 1.3 0.0 0.8 0.9 0.0 0.95 0.9 0.0 0.95 2.0 0.65 2.0 0.65
|
||||
pair_coeff * * oxdna2/hbond seqdep 0.0 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0.0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45
|
||||
|
||||
label loop
|
||||
variable base loop ${ntype}
|
||||
variable basemod equal ${base}%4
|
||||
if "${basemod} == 1" then &
|
||||
"variable comp equal ${base}+3" &
|
||||
"pair_coeff ${base} ${comp} oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45"
|
||||
if "${basemod} == 2" then &
|
||||
"variable comp equal ${base}+1" &
|
||||
"pair_coeff ${base} ${comp} oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45"
|
||||
next base
|
||||
jump in.duplex4.4type loop
|
||||
|
||||
pair_coeff * * oxdna2/xstk 3.9029021145006 4.89785 5.74965 4.21641 5.57929 2.25 0.791592654 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
|
||||
pair_coeff * * oxdna2/coaxstk 4.80673207785863 3.4072 5.1108 1.87396 4.94044 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793
|
||||
pair_coeff * * oxdna2/dh ${T} ${rhos} 0.815
|
||||
|
||||
# Langevin dynamics
|
||||
fix 1 all nve/asphere
|
||||
fix 2 all langevin ${T} ${T} 4265.0 457145 angmom 10
|
||||
|
||||
timestep 0.01706
|
||||
|
||||
#comm_style tiled
|
||||
fix 3 all balance 1000 1.03 shift xyz 10 1.03
|
||||
comm_modify cutoff 32.4
|
||||
|
||||
compute quat all property/atom quatw quati quatj quatk
|
||||
|
||||
compute erot all erotate/asphere
|
||||
compute ekin all ke
|
||||
compute epot all pe
|
||||
variable erot equal c_erot
|
||||
variable ekin equal c_ekin
|
||||
variable epot equal c_epot
|
||||
variable etot equal c_erot+c_ekin+c_epot
|
||||
fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
|
||||
|
||||
dump out all custom ${ofreq} out.${number}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz
|
||||
dump_modify out sort id
|
||||
dump_modify out format line "%d %d %d %22.15le %22.15le %22.15le %d %d %d %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le"
|
||||
|
||||
run 1000000
|
||||
|
||||
write_data last_config.${number}.* nocoeff
|
||||
#write_restart last_config.${number}.*
|
||||
@ -0,0 +1,87 @@
|
||||
variable number equal 8
|
||||
variable ofreq equal 1000
|
||||
variable efreq equal 1000
|
||||
|
||||
variable ntype equal 8
|
||||
|
||||
variable T equal 300.0
|
||||
variable rhos equal 0.2
|
||||
|
||||
units real
|
||||
|
||||
dimension 3
|
||||
|
||||
newton on
|
||||
|
||||
boundary p p p
|
||||
|
||||
atom_style hybrid bond ellipsoid oxdna
|
||||
atom_modify sort 0 8.518
|
||||
|
||||
# Pair interactions require lists of neighbours to be calculated
|
||||
neighbor 17.036 bin
|
||||
neigh_modify every 10 delay 0 check yes
|
||||
|
||||
read_data data.duplex4.8type
|
||||
|
||||
mass * 315.8376 # sets per-type mass if not in data file
|
||||
set atom * mass 315.8376 # sets per-atom mass
|
||||
|
||||
group all type 1 4
|
||||
|
||||
# oxDNA2 bond interactions - FENE backbone
|
||||
bond_style oxdna2/fene
|
||||
bond_coeff * 11.92337812042065 2.1295 6.4430152
|
||||
special_bonds lj 0 1 1
|
||||
|
||||
# oxDNA pair interactions
|
||||
pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
|
||||
pair_coeff * * oxdna2/excv 11.92337812042065 5.9626 5.74965 11.92337812042065 4.38677 4.259 11.92337812042065 2.81094 2.72576
|
||||
pair_coeff * * oxdna2/stk seqdep ${T} 8.06199211612242 0.005309213 0.70439070204273 3.4072 7.6662 2.72576 6.3885 1.3 0.0 0.8 0.9 0.0 0.95 0.9 0.0 0.95 2.0 0.65 2.0 0.65
|
||||
pair_coeff * * oxdna2/hbond seqdep 0.0 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0.0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45
|
||||
|
||||
label loop
|
||||
variable base loop ${ntype}
|
||||
variable basemod equal ${base}%4
|
||||
if "${basemod} == 1" then &
|
||||
"variable comp equal ${base}+3" &
|
||||
"pair_coeff ${base} ${comp} oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45"
|
||||
if "${basemod} == 2" then &
|
||||
"variable comp equal ${base}+1" &
|
||||
"pair_coeff ${base} ${comp} oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45"
|
||||
next base
|
||||
jump in.duplex4.8type loop
|
||||
|
||||
pair_coeff * * oxdna2/xstk 3.9029021145006 4.89785 5.74965 4.21641 5.57929 2.25 0.791592654 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
|
||||
pair_coeff * * oxdna2/coaxstk 4.80673207785863 3.4072 5.1108 1.87396 4.94044 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793
|
||||
pair_coeff * * oxdna2/dh ${T} ${rhos} 0.815
|
||||
|
||||
# Langevin dynamics
|
||||
fix 1 all nve/asphere
|
||||
fix 2 all langevin ${T} ${T} 4265.0 457145 angmom 10
|
||||
|
||||
timestep 0.01706
|
||||
|
||||
#comm_style tiled
|
||||
fix 3 all balance 1000 1.03 shift xyz 10 1.03
|
||||
comm_modify cutoff 32.4
|
||||
|
||||
compute quat all property/atom quatw quati quatj quatk
|
||||
|
||||
compute erot all erotate/asphere
|
||||
compute ekin all ke
|
||||
compute epot all pe
|
||||
variable erot equal c_erot
|
||||
variable ekin equal c_ekin
|
||||
variable epot equal c_epot
|
||||
variable etot equal c_erot+c_ekin+c_epot
|
||||
fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
|
||||
|
||||
dump out all custom ${ofreq} out.${number}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz
|
||||
dump_modify out sort id
|
||||
dump_modify out format line "%d %d %d %22.15le %22.15le %22.15le %d %d %d %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le"
|
||||
|
||||
run 1000000
|
||||
|
||||
write_data last_config.${number}.* nocoeff
|
||||
#write_restart last_config.${number}.*
|
||||
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
Some files were not shown because too many files have changed in this diff Show More
Reference in New Issue
Block a user