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rename CG-DNA potential files

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Axel Kohlmeyer
2024-06-20 14:33:26 -04:00
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100
doc/src/bond_oxdna.rst
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@ -38,7 +38,7 @@ Examples
bond_coeff * 2.0 0.25 0.76107
bond_style oxdna/fene
bond_coeff * oxdna.lj
bond_coeff * oxdna_lj.cgdna
# Real units
bond_style oxdna/fene
@ -51,14 +51,17 @@ Examples
bond_coeff * 11.92337812042065 2.1295 6.482800913
bond_style oxrna2/fene
bond_coeff * oxrna2.real
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.
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
"""""""""""
@ -70,15 +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)
@ -86,39 +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 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
@ -138,22 +141,33 @@ 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:
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
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:
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/.
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/``.
----------

161
doc/src/pair_oxdna.rst
View File

@ -60,13 +60,13 @@ Examples
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
pair_coeff * * oxdna/stk seqav 0.1 1.3448 2.6568 oxdna.lj
pair_coeff * * oxdna/hbond seqav oxdna.lj
pair_coeff 1 4 oxdna/hbond seqav oxdna.lj
pair_coeff 2 3 oxdna/hbond seqav oxdna.lj
pair_coeff * * oxdna/xstk oxdna.lj
pair_coeff * * oxdna/coaxstk oxdna.lj
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
@ -79,68 +79,85 @@ Examples
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
pair_coeff * * oxdna/stk seqav 300.0 8.01727944817084 0.005279604 oxdna.real
pair_coeff * * oxdna/hbond seqav oxdna.real
pair_coeff 1 4 oxdna/hbond seqav oxdna.real
pair_coeff 2 3 oxdna/hbond seqav oxdna.real
pair_coeff * * oxdna/xstk oxdna.real
pair_coeff * * oxdna/coaxstk oxdna.real
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.
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 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.
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>`,
@ -152,35 +169,51 @@ 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:
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
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:
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:
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
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
pair_coeff 1 4 oxdna/hbond seqav oxdna.lj
pair_coeff 2 3 oxdna/hbond seqav oxdna.lj
pair_coeff * * oxdna/xstk oxdna.lj
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*.
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/.
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/``.
----------

170
doc/src/pair_oxdna2.rst
View File

@ -69,14 +69,14 @@ Examples
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
pair_coeff * * oxdna2/stk seqdep 0.1 1.3523 2.6717 oxdna2.lj
pair_coeff * * oxdna2/hbond seqdep oxdna2.lj
pair_coeff 1 4 oxdna2/hbond seqdep oxdna2.lj
pair_coeff 2 3 oxdna2/hbond seqdep oxdna2.lj
pair_coeff * * oxdna2/xstk oxdna2.lj
pair_coeff * * oxdna2/coaxstk oxdna2.lj
pair_coeff * * oxdna2/dh 0.1 0.5 oxdna2.lj
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
@ -90,69 +90,88 @@ Examples
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
pair_coeff * * oxdna2/stk seqdep 300.0 8.06199211612242 0.005309213 oxdna2.real
pair_coeff * * oxdna2/hbond seqdep oxdna2.real
pair_coeff 1 4 oxdna2/hbond seqdep oxdna2.real
pair_coeff 2 3 oxdna2/hbond seqdep oxdna2.real
pair_coeff * * oxdna2/xstk oxdna2.real
pair_coeff * * oxdna2/coaxstk oxdna2.real
pair_coeff * * oxdna2/dh 300.0 0.5 oxdna2.real
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.
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 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.
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>`.
@ -162,38 +181,53 @@ Please cite also the relevant oxDNA2 publications
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:
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
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:
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:
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
pair_coeff * * oxdna2/hbond seqdep oxdna2.lj
pair_coeff 1 4 oxdna2/hbond seqdep oxdna2.lj
pair_coeff 2 3 oxdna2/hbond seqdep oxdna2.lj
pair_coeff * * oxdna2/xstk oxdna2.lj
pair_coeff * * oxdna2/coaxstk oxdna2.lj
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*.
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/.
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/``.
----------

180
doc/src/pair_oxrna2.rst
View File

@ -70,15 +70,15 @@ Examples
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
pair_coeff * * oxrna2/stk seqdep 0.1 1.40206 2.77 oxrna2.lj
pair_coeff * * oxrna2/hbond seqdep oxrna2.lj
pair_coeff 1 4 oxrna2/hbond seqdep oxrna2.lj
pair_coeff 2 3 oxrna2/hbond seqdep oxrna2.lj
pair_coeff 3 4 oxrna2/hbond seqdep oxrna2.lj
pair_coeff * * oxrna2/xstk oxrna2.lj
pair_coeff * * oxrna2/coaxstk oxrna2.lj
pair_coeff * * oxrna2/dh 0.1 0.5 oxrna2.lj
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
@ -93,112 +93,144 @@ Examples
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
pair_coeff * * oxrna2/stk seqdep 300.0 8.35864576375849 0.005504556 oxrna2.real
pair_coeff * * oxrna2/hbond seqdep oxrna2.real
pair_coeff 1 4 oxrna2/hbond seqdep oxrna2.real
pair_coeff 2 3 oxrna2/hbond seqdep oxrna2.real
pair_coeff 3 4 oxrna2/hbond seqdep oxrna2.real
pair_coeff * * oxrna2/xstk oxrna2.real
pair_coeff * * oxrna2/coaxstk oxrna2.real
pair_coeff * * oxrna2/dh 300.0 0.5 oxrna2.real
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.
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 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
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 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.
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:
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
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:
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:
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
pair_coeff * * oxrna2/hbond seqdep oxrna2.lj
pair_coeff 1 4 oxrna2/hbond seqdep oxrna2.lj
pair_coeff 2 3 oxrna2/hbond seqdep oxrna2.lj
pair_coeff 3 4 oxrna2/hbond seqdep oxrna2.lj
pair_coeff * * oxrna2/xstk oxrna2.lj
pair_coeff * * oxrna2/coaxstk oxrna2.lj
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*.
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/.
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/``.
----------

16
examples/PACKAGES/cgdna/examples/lj_units/oxDNA/potential_file/in.duplex1
View File

@ -26,18 +26,18 @@ group all type 1 4
# oxDNA bond interactions - FENE backbone
bond_style oxdna/fene
bond_coeff * oxdna.lj
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
pair_coeff * * oxdna/stk seqav 0.1 1.3448 2.6568 oxdna.lj
pair_coeff * * oxdna/hbond seqav oxdna.lj
pair_coeff 1 4 oxdna/hbond seqav oxdna.lj
pair_coeff 2 3 oxdna/hbond seqav oxdna.lj
pair_coeff * * oxdna/xstk oxdna.lj
pair_coeff * * oxdna/coaxstk oxdna.lj
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

1
examples/PACKAGES/cgdna/examples/lj_units/oxDNA/potential_file/oxdna_lj.cgdna Symbolic link
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@ -0,0 +1 @@
../../../../../../../potentials/oxdna_lj.cgdna

18
examples/PACKAGES/cgdna/examples/lj_units/oxDNA2/potential_file/in.duplex1
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@ -27,19 +27,19 @@ group all type 1 4
# oxDNA2 bond interactions - FENE backbone
bond_style oxdna2/fene
bond_coeff * oxdna2.lj
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
pair_coeff * * oxdna2/stk seqdep 0.1 1.3523 2.6717 oxdna2.lj
pair_coeff * * oxdna2/hbond seqdep oxdna2.lj
pair_coeff 1 4 oxdna2/hbond seqdep oxdna2.lj
pair_coeff 2 3 oxdna2/hbond seqdep oxdna2.lj
pair_coeff * * oxdna2/xstk oxdna2.lj
pair_coeff * * oxdna2/coaxstk oxdna2.lj
pair_coeff * * oxdna2/dh 0.1 0.5 oxdna2.lj
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

1
examples/PACKAGES/cgdna/examples/lj_units/oxDNA2/potential_file/oxdna2_lj.cgdna Symbolic link
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@ -0,0 +1 @@
../../../../../../../potentials/oxdna2_lj.cgdna

20
examples/PACKAGES/cgdna/examples/lj_units/oxRNA2/potential_file/in.duplex2
View File

@ -27,20 +27,20 @@ group all type 1 4
# oxRNA2 bond interactions - FENE backbone
bond_style oxrna2/fene
bond_coeff * oxrna2.lj
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
pair_coeff * * oxrna2/stk seqdep 0.1 1.40206 2.77 oxrna2.lj
pair_coeff * * oxrna2/hbond seqdep oxrna2.lj
pair_coeff 1 4 oxrna2/hbond seqdep oxrna2.lj
pair_coeff 2 3 oxrna2/hbond seqdep oxrna2.lj
pair_coeff 3 4 oxrna2/hbond seqdep oxrna2.lj
pair_coeff * * oxrna2/xstk oxrna2.lj
pair_coeff * * oxrna2/coaxstk oxrna2.lj
pair_coeff * * oxrna2/dh 0.1 0.5 oxrna2.lj
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

1
examples/PACKAGES/cgdna/examples/lj_units/oxRNA2/potential_file/oxrna2_lj.cgdna Symbolic link
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@ -0,0 +1 @@
../../../../../../../potentials/oxrna2_lj.cgdna

16
examples/PACKAGES/cgdna/examples/real_units/oxDNA/potential_file/in.duplex1
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@ -27,18 +27,18 @@ group all type 1 4
# oxDNA bond interactions - FENE backbone
bond_style oxdna/fene
bond_coeff * oxdna.real
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
pair_coeff * * oxdna/stk seqav ${T} 8.01727944817084 0.005279604 oxdna.real
pair_coeff * * oxdna/hbond seqav oxdna.real
pair_coeff 1 4 oxdna/hbond seqav oxdna.real
pair_coeff 2 3 oxdna/hbond seqav oxdna.real
pair_coeff * * oxdna/xstk oxdna.real
pair_coeff * * oxdna/coaxstk oxdna.real
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

1
examples/PACKAGES/cgdna/examples/real_units/oxDNA/potential_file/oxdna_real.cgdna Symbolic link
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@ -0,0 +1 @@
../../../../../../../potentials/oxdna_real.cgdna

18
examples/PACKAGES/cgdna/examples/real_units/oxDNA2/potential_file/in.duplex1
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@ -28,19 +28,19 @@ group all type 1 4
# oxDNA2 bond interactions - FENE backbone
bond_style oxdna2/fene
bond_coeff * oxdna2.real
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
pair_coeff * * oxdna2/stk seqav 300.0 8.06199211612242 0.005309213 oxdna2.real
pair_coeff * * oxdna2/hbond seqav oxdna2.real
pair_coeff 1 4 oxdna2/hbond seqav oxdna2.real
pair_coeff 2 3 oxdna2/hbond seqav oxdna2.real
pair_coeff * * oxdna2/xstk oxdna2.real
pair_coeff * * oxdna2/coaxstk oxdna2.real
pair_coeff * * oxdna2/dh 300.0 0.5 oxdna2.real
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

1
examples/PACKAGES/cgdna/examples/real_units/oxDNA2/potential_file/oxdna2_real.cgdna Symbolic link
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@ -0,0 +1 @@
../../../../../../../potentials/oxdna2_real.cgdna

20
examples/PACKAGES/cgdna/examples/real_units/oxRNA2/potential_file/in.duplex2
View File

@ -28,20 +28,20 @@ group all type 1 4
# oxRNA2 bond interactions - FENE backbone
bond_style oxrna2/fene
bond_coeff * oxrna2.real
bond_coeff * oxrna2_real.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.real
pair_coeff * * oxrna2/stk seqdep 300.0 8.35864576375849 0.005504556 oxrna2.real
pair_coeff * * oxrna2/hbond seqdep oxrna2.real
pair_coeff 1 4 oxrna2/hbond seqdep oxrna2.real
pair_coeff 2 3 oxrna2/hbond seqdep oxrna2.real
pair_coeff 3 4 oxrna2/hbond seqdep oxrna2.real
pair_coeff * * oxrna2/xstk oxrna2.real
pair_coeff * * oxrna2/coaxstk oxrna2.real
pair_coeff * * oxrna2/dh 300.0 0.5 oxrna2.real
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
# NVE ensemble
fix 1 all nve/asphere

1
examples/PACKAGES/cgdna/examples/real_units/oxRNA2/potential_file/oxrna2_real.cgdna Symbolic link
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@ -0,0 +1 @@
../../../../../../../potentials/oxrna2_real.cgdna

1
potentials/README
View File

@ -87,6 +87,7 @@ adp ADP angular dependent potential
airebo AI-REBO potentials
bop.table BOP potential, tabulated form
cdeam concentration-dependent EAM
cgdna potential files for styles in the CG-DNA package
comb COMB potential
comb3 COMB3 potential
eam embedded atom method (EAM) single element, DYNAMO funcfl format

0
potentials/oxdna2.lj → potentials/oxdna2_lj.cgdna
View File

0
potentials/oxdna2.real → potentials/oxdna2_real.cgdna
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0
potentials/oxdna.lj → potentials/oxdna_lj.cgdna
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0
potentials/oxdna.real → potentials/oxdna_real.cgdna
View File

0
potentials/oxrna2.lj → potentials/oxrna2_lj.cgdna
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0
potentials/oxrna2.real → potentials/oxrna2_real.cgdna
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22
purge-workflows.py Normal file
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@ -0,0 +1,22 @@
from yaml import load
import subprocess
try:
from yaml import CLoader as Loader
except ImportError:
from yaml import Loader
runs = subprocess.check_output('gh api repos/lammps/lammps/actions/runs',shell=True)
data = load(runs,Loader=Loader)
while data['total_count'] > 3:
print('remaining: ', data['total_count'])
num=1
for d in data['workflow_runs']:
print(num, d['id'],d['name'],d['run_number'])
num += 1
if num > 4:
subprocess.call('gh api -X DELETE repos/lammps/lammps/actions/runs/' + str(d['id']), shell=True)
#print('gh api -X DELETE repos/lammps/lammps/actions/runs/' + str(d['id']))
else:
print('skip')
runs = subprocess.check_output('gh api repos/lammps/lammps/actions/runs',shell=True)
data = load(runs,Loader=Loader)

2
src/CG-DNA/pair_oxdna2_dh.cpp
View File

@ -307,7 +307,7 @@ void PairOxdna2Dh::coeff(int narg, char **arg)
T = utils::numeric(FLERR,arg[2],false,lmp);
rhos_dh_one = utils::numeric(FLERR,arg[3],false,lmp);
if (utils::strmatch(arg[4], "^[a-zA-Z0-9]*\\.[a-zA-Z]+$") == true) { // if last arg is a potential file
if (utils::strmatch(arg[4], "^[a-zA-Z0-9_]*\\.cgdna$")) { // if last arg is a potential file
if (comm->me == 0) { // read value from potential file
PotentialFileReader reader(lmp, arg[4], "oxdna potential", " (dh)");
char * line;