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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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doc/src/bond_oxdna.rst
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@ -38,7 +38,7 @@ Examples
bond_coeff * 2.0 0.25 0.76107 bond_coeff * 2.0 0.25 0.76107
bond_style oxdna/fene bond_style oxdna/fene
bond_coeff * oxdna.lj bond_coeff * oxdna_lj.cgdna
# Real units # Real units
bond_style oxdna/fene bond_style oxdna/fene
@ -51,14 +51,17 @@ Examples
bond_coeff * 11.92337812042065 2.1295 6.482800913 bond_coeff * 11.92337812042065 2.1295 6.482800913
bond_style oxrna2/fene bond_style oxrna2/fene
bond_coeff * oxrna2.real bond_coeff * oxrna2_real.cgdna
.. note:: .. 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 The coefficients in the above examples have to be kept fixed and
compatible with both *units lj* and *units real* (see documentation of :doc:`units <units>`). cannot be changed without reparameterizing the entire model. They are
These can also be read from a potential file with correct unit style by specifying the name provided in forms compatible with both *units lj* and *units real*
of the file. Several potential files for each unit style are included in the /potentials/ directory of the LAMMPS distribution. (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 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] 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) to define a modified finite extensible nonlinear elastic (FENE)
potential :ref:`(Ouldridge) <Ouldridge0>` to model the connectivity of the potential :ref:`(Ouldridge) <Ouldridge0>` to model the connectivity of
phosphate backbone in the oxDNA/oxRNA force field for coarse-grained the phosphate backbone in the oxDNA/oxRNA force field for coarse-grained
modelling of DNA/RNA. modelling of DNA/RNA.
The following coefficients must be defined for the bond type via the 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 :doc:`bond_coeff <bond_coeff>` command as given in the above example, or
in the data file or restart files read by the in the data file or restart files read by the :doc:`read_data
:doc:`read_data <read_data>` or :doc:`read_restart <read_restart>` <read_data>` or :doc:`read_restart <read_restart>` commands:
commands:
* :math:`\epsilon` (energy) * :math:`\epsilon` (energy)
* :math:`\Delta` (distance) * :math:`\Delta` (distance)
@ -86,39 +88,40 @@ commands:
.. note:: .. note::
The oxDNA bond style has to be used together with the The oxDNA bond style has to be used together with the corresponding
corresponding oxDNA pair styles for excluded volume interaction oxDNA pair styles for excluded volume interaction *oxdna/excv* ,
*oxdna/excv* , stacking *oxdna/stk* , cross-stacking *oxdna/xstk* and stacking *oxdna/stk* , cross-stacking *oxdna/xstk* and coaxial
coaxial stacking interaction *oxdna/coaxstk* as well as stacking interaction *oxdna/coaxstk* as well as hydrogen-bonding
hydrogen-bonding interaction *oxdna/hbond* (see also documentation of interaction *oxdna/hbond* (see also documentation of :doc:`pair_style
:doc:`pair_style oxdna/excv <pair_oxdna>`). For the oxDNA2 oxdna/excv <pair_oxdna>`). For the oxDNA2 :ref:`(Snodin) <Snodin0>`
:ref:`(Snodin) <Snodin0>` bond style the analogous pair styles bond style the analogous pair styles *oxdna2/excv* , *oxdna2/stk* ,
*oxdna2/excv* , *oxdna2/stk* , *oxdna2/xstk* , *oxdna2/coaxstk* , *oxdna2/xstk* , *oxdna2/coaxstk* , *oxdna2/hbond* and an additional
*oxdna2/hbond* and an additional Debye-Hueckel pair style Debye-Hueckel pair style *oxdna2/dh* have to be defined. The same
*oxdna2/dh* have to be defined. The same applies to the oxRNA2 applies to the oxRNA2 :ref:`(Sulc1) <Sulc01>` styles.
:ref:`(Sulc1) <Sulc01>` styles.
.. note:: .. note::
This bond style has to be used with the *atom_style hybrid bond ellipsoid oxdna* This bond style has to be used with the *atom_style hybrid bond
(see documentation of :doc:`atom_style <atom_style>`). The *atom_style oxdna* ellipsoid oxdna* (see documentation of :doc:`atom_style
stores the 3'-to-5' polarity of the nucleotide strand, which is set through <atom_style>`). The *atom_style oxdna* stores the 3'-to-5' polarity
the bond topology in the data file. The first (second) atom in a bond definition of the nucleotide strand, which is set through the bond topology in
is understood to point towards the 3'-end (5'-end) of the strand. 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:: .. warning::
If data files are produced with :doc:`write_data <write_data>`, then the If data files are produced with :doc:`write_data <write_data>`, then
:doc:`newton <newton>` command should be set to *newton on* or *newton off on*. the :doc:`newton <newton>` command should be set to *newton on* or
Otherwise the data files will not have the same 3'-to-5' polarity as the *newton off on*. Otherwise the data files will not have the same
initial data file. This limitation does not apply to binary restart files 3'-to-5' polarity as the initial data file. This limitation does not
produced with :doc:`write_restart <write_restart>`. 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 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 ``examples/PACKAGES/cgdna/examples/oxDNA/`, `.../oxDNA2/`` and
setup tool which creates single straight or helical DNA strands, DNA/RNA ``.../oxRNA2/``. A simple python setup tool which creates single
duplexes or arrays of DNA/RNA duplexes can be found in straight or helical DNA strands, DNA/RNA duplexes or arrays of DNA/RNA
examples/PACKAGES/cgdna/util/. duplexes can be found in ``examples/PACKAGES/cgdna/util/``.
Please cite :ref:`(Henrich) <Henrich0>` in any publication that uses Please cite :ref:`(Henrich) <Henrich0>` in any publication that uses
this implementation. An updated documentation that contains general information 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 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 .. code-block:: LAMMPS
bond_style oxdna/fene 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. will be interpreted as a request to read the (FENE) potential
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: :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 .. code-block:: LAMMPS
* fene epsilon delta r0 * 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 There are sample potential files for each unit style in the
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/. ``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
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@ -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_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_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 oxdna.lj pair_coeff * * oxdna/stk seqav 0.1 1.3448 2.6568 oxdna_lj.cgdna
pair_coeff * * oxdna/hbond seqav oxdna.lj pair_coeff * * oxdna/hbond seqav oxdna_lj.cgdna
pair_coeff 1 4 oxdna/hbond seqav oxdna.lj pair_coeff 1 4 oxdna/hbond seqav oxdna_lj.cgdna
pair_coeff 2 3 oxdna/hbond seqav oxdna.lj pair_coeff 2 3 oxdna/hbond seqav oxdna_lj.cgdna
pair_coeff * * oxdna/xstk oxdna.lj pair_coeff * * oxdna/xstk oxdna_lj.cgdna
pair_coeff * * oxdna/coaxstk oxdna.lj pair_coeff * * oxdna/coaxstk oxdna_lj.cgdna
# Real units # Real units
pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk 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_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_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk
pair_coeff * * oxdna/excv oxdna.real pair_coeff * * oxdna/excv oxdna_real.cgdna
pair_coeff * * oxdna/stk seqav 300.0 8.01727944817084 0.005279604 oxdna.real pair_coeff * * oxdna/stk seqav 300.0 8.01727944817084 0.005279604 oxdna_real.cgdna
pair_coeff * * oxdna/hbond seqav oxdna.real pair_coeff * * oxdna/hbond seqav oxdna_real.cgdna
pair_coeff 1 4 oxdna/hbond seqav oxdna.real pair_coeff 1 4 oxdna/hbond seqav oxdna_real.cgdna
pair_coeff 2 3 oxdna/hbond seqav oxdna.real pair_coeff 2 3 oxdna/hbond seqav oxdna_real.cgdna
pair_coeff * * oxdna/xstk oxdna.real pair_coeff * * oxdna/xstk oxdna_real.cgdna
pair_coeff * * oxdna/coaxstk oxdna.real pair_coeff * * oxdna/coaxstk oxdna_real.cgdna
.. note:: .. 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>`). The coefficients in the above examples are provided in forms
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. 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 Description
""""""""""" """""""""""
The *oxdna* pair styles compute the pairwise-additive parts of the oxDNA force field The *oxdna* pair styles compute the pairwise-additive parts of the oxDNA
for coarse-grained modelling of DNA. The effective interaction between the nucleotides consists of potentials for the force field for coarse-grained modelling of DNA. The effective
excluded volume interaction *oxdna/excv*, the stacking *oxdna/stk*, cross-stacking *oxdna/xstk* interaction between the nucleotides consists of potentials for the
and coaxial stacking interaction *oxdna/coaxstk* as well excluded volume interaction *oxdna/excv*, the stacking *oxdna/stk*,
as the hydrogen-bonding interaction *oxdna/hbond* between complementary pairs of nucleotides on cross-stacking *oxdna/xstk* and coaxial stacking interaction
opposite strands. Average sequence or sequence-dependent stacking and base-pairing strengths *oxdna/coaxstk* as well as the hydrogen-bonding interaction
are supported :ref:`(Sulc) <Sulc1>`. Quasi-unique base-pairing between nucleotides can be achieved by using *oxdna/hbond* between complementary pairs of nucleotides on opposite
more complementary pairs of atom types like 5-8 and 6-7, 9-12 and 10-11, 13-16 and 14-15, etc. strands. Average sequence or sequence-dependent stacking and
This prevents the hybridization of in principle complementary bases within Ntypes/4 bases base-pairing strengths are supported :ref:`(Sulc) <Sulc1>`. Quasi-unique
up and down along the backbone. 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 exact functional form of the pair styles is rather complex. The
The individual potentials consist of products of modulation factors, individual potentials consist of products of modulation factors, which
which themselves are constructed from a number of more basic potentials 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. (Morse, Lennard-Jones, harmonic angle and distance) as well as quadratic
We refer to :ref:`(Ouldridge-DPhil) <Ouldridge-DPhil1>` and :ref:`(Ouldridge) <Ouldridge1>` smoothing and modulation terms. We refer to :ref:`(Ouldridge-DPhil)
for a detailed description of the oxDNA force field. <Ouldridge-DPhil1>` and :ref:`(Ouldridge) <Ouldridge1>` for a detailed
description of the oxDNA force field.
.. note:: .. note::
These pair styles have to be used together with the related oxDNA bond style These pair styles have to be used together with the related oxDNA
*oxdna/fene* for the connectivity of the phosphate backbone (see also documentation of bond style *oxdna/fene* for the connectivity of the phosphate
:doc:`bond_style oxdna/fene <bond_oxdna>`). Most of the coefficients backbone (see also documentation of :doc:`bond_style oxdna/fene
in the above example have to be kept fixed and cannot be changed without reparameterizing the entire model. <bond_oxdna>`). Most of the coefficients in the above example have to
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) be kept fixed and cannot be changed without reparameterizing the
and the first coefficient after *oxdna/hbond* (seq=seqdep in the above example). entire model. Exceptions are the first four coefficients after
When using a Langevin thermostat, e.g. through :doc:`fix langevin <fix_langevin>` *oxdna/stk* (seq=seqdep, T=0.1, xi=1.3448 and kappa=2.6568 and
or :doc:`fix nve/dotc/langevin <fix_nve_dotc_langevin>` corresponding *real unit* equivalents in the above examples) and the
the temperature coefficients have to be matched to the one used in the fix. 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:: .. note::
These pair styles have to be used with the *atom_style hybrid bond ellipsoid oxdna* These pair styles have to be used with the *atom_style hybrid bond
(see documentation of :doc:`atom_style <atom_style>`). The *atom_style oxdna* ellipsoid oxdna* (see documentation of :doc:`atom_style
stores the 3'-to-5' polarity of the nucleotide strand, which is set through <atom_style>`). The *atom_style oxdna* stores the 3'-to-5' polarity
the bond topology in the data file. The first (second) atom in a bond definition of the nucleotide strand, which is set through the bond topology in
is understood to point towards the 3'-end (5'-end) of the strand. 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/. Example input and data files for DNA duplexes can be found in
A simple python setup tool which creates single straight or helical DNA strands, ``examples/PACKAGES/cgdna/examples/oxDNA/`` and ``.../oxDNA2/``. A
DNA duplexes or arrays of DNA duplexes can be found in examples/PACKAGES/cgdna/util/. 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 Please cite :ref:`(Henrich) <Henrich1>` in any publication that uses
this implementation. An updated documentation that contains general information this implementation. An updated documentation that contains general
on the model, its implementation and performance as well as the structure of information on the model, its implementation and performance as well as
the data and input file can be found `here <PDF/CG-DNA.pdf>`_. the structure of the data and input file can be found `here
<PDF/CG-DNA.pdf>`_.
Please cite also the relevant oxDNA publications Please cite also the relevant oxDNA publications
:ref:`(Ouldridge) <Ouldridge1>`, :ref:`(Ouldridge) <Ouldridge1>`,
@ -152,35 +169,51 @@ and :ref:`(Sulc) <Sulc1>`.
Potential file reading 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 .. 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 .. code-block:: LAMMPS
1 4 hbond <coefficients> 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 .. code-block:: LAMMPS
pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk 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/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 * * oxdna/hbond seqav oxdna_lj.cgdna
pair_coeff 1 4 oxdna/hbond seqav oxdna.lj pair_coeff 1 4 oxdna/hbond seqav oxdna_lj.cgdna
pair_coeff 2 3 oxdna/hbond seqav oxdna.lj pair_coeff 2 3 oxdna/hbond seqav oxdna_lj.cgdna
pair_coeff * * oxdna/xstk oxdna.lj 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 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 There are sample potential files for each unit style in the
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/. ``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
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@ -69,14 +69,14 @@ Examples
pair_coeff * * oxdna2/dh 0.1 0.5 0.815 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_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
pair_coeff * * oxdna2/excv oxdna2.lj pair_coeff * * oxdna2/excv oxdna2_lj.cgdna
pair_coeff * * oxdna2/stk seqdep 0.1 1.3523 2.6717 oxdna2.lj pair_coeff * * oxdna2/stk seqdep 0.1 1.3523 2.6717 oxdna2_lj.cgdna
pair_coeff * * oxdna2/hbond seqdep oxdna2.lj pair_coeff * * oxdna2/hbond seqdep oxdna2_lj.cgdna
pair_coeff 1 4 oxdna2/hbond seqdep oxdna2.lj pair_coeff 1 4 oxdna2/hbond seqdep oxdna2_lj.cgdna
pair_coeff 2 3 oxdna2/hbond seqdep oxdna2.lj pair_coeff 2 3 oxdna2/hbond seqdep oxdna2_lj.cgdna
pair_coeff * * oxdna2/xstk oxdna2.lj pair_coeff * * oxdna2/xstk oxdna2_lj.cgdna
pair_coeff * * oxdna2/coaxstk oxdna2.lj pair_coeff * * oxdna2/coaxstk oxdna2_lj.cgdna
pair_coeff * * oxdna2/dh 0.1 0.5 oxdna2.lj pair_coeff * * oxdna2/dh 0.1 0.5 oxdna2_lj.cgdna
# Real units # Real units
pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh 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_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_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
pair_coeff * * oxdna2/excv oxdna2.real pair_coeff * * oxdna2/excv oxdna2_real.cgdna
pair_coeff * * oxdna2/stk seqdep 300.0 8.06199211612242 0.005309213 oxdna2.real pair_coeff * * oxdna2/stk seqdep 300.0 8.06199211612242 0.005309213 oxdna2_real.cgdna
pair_coeff * * oxdna2/hbond seqdep oxdna2.real pair_coeff * * oxdna2/hbond seqdep oxdna2_real.cgdna
pair_coeff 1 4 oxdna2/hbond seqdep oxdna2.real pair_coeff 1 4 oxdna2/hbond seqdep oxdna2_real.cgdna
pair_coeff 2 3 oxdna2/hbond seqdep oxdna2.real pair_coeff 2 3 oxdna2/hbond seqdep oxdna2_real.cgdna
pair_coeff * * oxdna2/xstk oxdna2.real pair_coeff * * oxdna2/xstk oxdna2_real.cgdna
pair_coeff * * oxdna2/coaxstk oxdna2.real pair_coeff * * oxdna2/coaxstk oxdna2_real.cgdna
pair_coeff * * oxdna2/dh 300.0 0.5 oxdna2.real pair_coeff * * oxdna2/dh 300.0 0.5 oxdna2_real.cgdna
.. note:: .. 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>`). The coefficients in the above examples are provided in forms
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. 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 Description
""""""""""" """""""""""
The *oxdna2* pair styles compute the pairwise-additive parts of the oxDNA force field The *oxdna2* pair styles compute the pairwise-additive parts of the
for coarse-grained modelling of DNA. The effective interaction between the nucleotides consists of potentials for the oxDNA force field for coarse-grained modelling of DNA. The effective
excluded volume interaction *oxdna2/excv*, the stacking *oxdna2/stk*, cross-stacking *oxdna2/xstk* interaction between the nucleotides consists of potentials for the
and coaxial stacking interaction *oxdna2/coaxstk*, electrostatic Debye-Hueckel interaction *oxdna2/dh* excluded volume interaction *oxdna2/excv*, the stacking *oxdna2/stk*,
as well as the hydrogen-bonding interaction *oxdna2/hbond* between complementary pairs of nucleotides on cross-stacking *oxdna2/xstk* and coaxial stacking interaction
opposite strands. Average sequence or sequence-dependent stacking and base-pairing strengths *oxdna2/coaxstk*, electrostatic Debye-Hueckel interaction *oxdna2/dh* as
are supported :ref:`(Sulc) <Sulc2>`. Quasi-unique base-pairing between nucleotides can be achieved by using well as the hydrogen-bonding interaction *oxdna2/hbond* between
more complementary pairs of atom types like 5-8 and 6-7, 9-12 and 10-11, 13-16 and 14-15, etc. complementary pairs of nucleotides on opposite strands. Average sequence
This prevents the hybridization of in principle complementary bases within Ntypes/4 bases 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. up and down along the backbone.
The exact functional form of the pair styles is rather complex. The exact functional form of the pair styles is rather complex. The
The individual potentials consist of products of modulation factors, individual potentials consist of products of modulation factors, which
which themselves are constructed from a number of more basic potentials 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. (Morse, Lennard-Jones, harmonic angle and distance) as well as quadratic
We refer to :ref:`(Snodin) <Snodin2>` and the original oxDNA publications :ref:`(Ouldridge-DPhil) <Ouldridge-DPhil2>` smoothing and modulation terms. We refer to :ref:`(Snodin) <Snodin2>`
and :ref:`(Ouldridge) <Ouldridge2>` for a detailed description of the oxDNA2 force field. and the original oxDNA publications :ref:`(Ouldridge-DPhil)
<Ouldridge-DPhil2>` and :ref:`(Ouldridge) <Ouldridge2>` for a detailed
description of the oxDNA2 force field.
.. note:: .. note::
These pair styles have to be used together with the related oxDNA2 bond style These pair styles have to be used together with the related oxDNA2
*oxdna2/fene* for the connectivity of the phosphate backbone (see also documentation of bond style *oxdna2/fene* for the connectivity of the phosphate
:doc:`bond_style oxdna2/fene <bond_oxdna>`). Most of the coefficients backbone (see also documentation of :doc:`bond_style oxdna2/fene
in the above example have to be kept fixed and cannot be changed without reparameterizing the entire model. <bond_oxdna>`). Most of the coefficients in the above example have to
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). be kept fixed and cannot be changed without reparameterizing the
the first coefficient after *oxdna2/hbond* (seq=seqdep in the above example) and the three coefficients entire model. Exceptions are the first four coefficients after
after *oxdna2/dh* (T=0.1, rhos=0.5, qeff=0.815 in the above example). When using a Langevin thermostat *oxdna2/stk* (seq=seqdep, T=0.1, xi=1.3523 and kappa=2.6717 and
e.g. through :doc:`fix langevin <fix_langevin>` or :doc:`fix nve/dotc/langevin <fix_nve_dotc_langevin>` corresponding *real unit* equivalents in the above examples). the
the temperature coefficients have to be matched to the one used in the fix. 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:: .. note::
These pair styles have to be used with the *atom_style hybrid bond ellipsoid oxdna* These pair styles have to be used with the *atom_style hybrid bond
(see documentation of :doc:`atom_style <atom_style>`). The *atom_style oxdna* ellipsoid oxdna* (see documentation of :doc:`atom_style
stores the 3'-to-5' polarity of the nucleotide strand, which is set through <atom_style>`). The *atom_style oxdna* stores the 3'-to-5' polarity
the bond topology in the data file. The first (second) atom in a bond definition of the nucleotide strand, which is set through the bond topology in
is understood to point towards the 3'-end (5'-end) of the strand. 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/. Example input and data files for DNA duplexes can be found in
A simple python setup tool which creates single straight or helical DNA strands, ``examples/PACKAGES/cgdna/examples/oxDNA/`` and ``.../oxDNA2/``. A
DNA duplexes or arrays of DNA duplexes can be found in examples/PACKAGES/cgdna/util/. 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 Please cite :ref:`(Henrich) <Henrich2>` in any publication that uses
this implementation. An updated documentation that contains general information this implementation. An updated documentation that contains general
on the model, its implementation and performance as well as the structure of information on the model, its implementation and performance as well as
the data and input file can be found `here <PDF/CG-DNA.pdf>`_. the structure of the data and input file can be found `here
<PDF/CG-DNA.pdf>`_.
Please cite also the relevant oxDNA2 publications Please cite also the relevant oxDNA2 publications
:ref:`(Snodin) <Snodin2>` and :ref:`(Sulc) <Sulc2>`. :ref:`(Snodin) <Snodin2>` and :ref:`(Sulc) <Sulc2>`.
@ -162,38 +181,53 @@ Please cite also the relevant oxDNA2 publications
Potential file reading 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. For each pair style above the first non-modifiable argument can be a
Therefore the following command: 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 .. 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. will be interpreted as a request to read the corresponding hydrogen
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: 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 .. code-block:: LAMMPS
1 4 hbond <coefficients> 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 .. code-block:: LAMMPS
pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh 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/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/stk seqdep 0.1 1.3523 2.6717 oxdna2_lj.cgdna
pair_coeff * * oxdna2/hbond seqdep oxdna2.lj pair_coeff * * oxdna2/hbond seqdep oxdna2_lj.cgdna
pair_coeff 1 4 oxdna2/hbond seqdep oxdna2.lj pair_coeff 1 4 oxdna2/hbond seqdep oxdna2_lj.cgdna
pair_coeff 2 3 oxdna2/hbond seqdep oxdna2.lj pair_coeff 2 3 oxdna2/hbond seqdep oxdna2_lj.cgdna
pair_coeff * * oxdna2/xstk oxdna2.lj pair_coeff * * oxdna2/xstk oxdna2_lj.cgdna
pair_coeff * * oxdna2/coaxstk oxdna2.lj pair_coeff * * oxdna2/coaxstk oxdna2_lj.cgdna
pair_coeff * * oxdna2/dh 0.1 0.5 0.815 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 There are sample potential files for each unit style in the ``potentials``
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/. 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_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_style hybrid/overlay oxrna2/excv oxrna2/stk oxrna2/hbond oxrna2/xstk oxrna2/coaxstk oxrna2/dh
pair_coeff * * oxrna2/excv oxrna2.lj pair_coeff * * oxrna2/excv oxrna2_lj.cgdna
pair_coeff * * oxrna2/stk seqdep 0.1 1.40206 2.77 oxrna2.lj pair_coeff * * oxrna2/stk seqdep 0.1 1.40206 2.77 oxrna2_lj.cgdna
pair_coeff * * oxrna2/hbond seqdep oxrna2.lj pair_coeff * * oxrna2/hbond seqdep oxrna2_lj.cgdna
pair_coeff 1 4 oxrna2/hbond seqdep oxrna2.lj pair_coeff 1 4 oxrna2/hbond seqdep oxrna2_lj.cgdna
pair_coeff 2 3 oxrna2/hbond seqdep oxrna2.lj pair_coeff 2 3 oxrna2/hbond seqdep oxrna2_lj.cgdna
pair_coeff 3 4 oxrna2/hbond seqdep oxrna2.lj pair_coeff 3 4 oxrna2/hbond seqdep oxrna2_lj.cgdna
pair_coeff * * oxrna2/xstk oxrna2.lj pair_coeff * * oxrna2/xstk oxrna2_lj.cgdna
pair_coeff * * oxrna2/coaxstk oxrna2.lj pair_coeff * * oxrna2/coaxstk oxrna2_lj.cgdna
pair_coeff * * oxrna2/dh 0.1 0.5 oxrna2.lj pair_coeff * * oxrna2/dh 0.1 0.5 oxrna2_lj.cgdna
# Real units # Real units
pair_style hybrid/overlay oxrna2/excv oxrna2/stk oxrna2/hbond oxrna2/xstk oxrna2/coaxstk oxrna2/dh 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_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_style hybrid/overlay oxrna2/excv oxrna2/stk oxrna2/hbond oxrna2/xstk oxrna2/coaxstk oxrna2/dh
pair_coeff * * oxrna2/excv oxrna2.real pair_coeff * * oxrna2/excv oxrna2_real.cgdna
pair_coeff * * oxrna2/stk seqdep 300.0 8.35864576375849 0.005504556 oxrna2.real pair_coeff * * oxrna2/stk seqdep 300.0 8.35864576375849 0.005504556 oxrna2_real.cgdna
pair_coeff * * oxrna2/hbond seqdep oxrna2.real pair_coeff * * oxrna2/hbond seqdep oxrna2_real.cgdna
pair_coeff 1 4 oxrna2/hbond seqdep oxrna2.real pair_coeff 1 4 oxrna2/hbond seqdep oxrna2_real.cgdna
pair_coeff 2 3 oxrna2/hbond seqdep oxrna2.real pair_coeff 2 3 oxrna2/hbond seqdep oxrna2_real.cgdna
pair_coeff 3 4 oxrna2/hbond seqdep oxrna2.real pair_coeff 3 4 oxrna2/hbond seqdep oxrna2_real.cgdna
pair_coeff * * oxrna2/xstk oxrna2.real pair_coeff * * oxrna2/xstk oxrna2_real.cgdna
pair_coeff * * oxrna2/coaxstk oxrna2.real pair_coeff * * oxrna2/coaxstk oxrna2_real.cgdna
pair_coeff * * oxrna2/dh 300.0 0.5 oxrna2.real pair_coeff * * oxrna2/dh 300.0 0.5 oxrna2_real.cgdna
.. note:: .. 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>`). The coefficients in the above examples are provided in forms
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. 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 Description
""""""""""" """""""""""
The *oxrna2* pair styles compute the pairwise-additive parts of the oxDNA force field The *oxrna2* pair styles compute the pairwise-additive parts of the
for coarse-grained modelling of RNA. The effective interaction between the nucleotides consists of potentials for the oxDNA force field for coarse-grained modelling of RNA. The effective
excluded volume interaction *oxrna2/excv*, the stacking *oxrna2/stk*, cross-stacking *oxrna2/xstk* interaction between the nucleotides consists of potentials for the
and coaxial stacking interaction *oxrna2/coaxstk*, electrostatic Debye-Hueckel interaction *oxrna2/dh* excluded volume interaction *oxrna2/excv*, the stacking *oxrna2/stk*,
as well as the hydrogen-bonding interaction *oxrna2/hbond* between complementary pairs of nucleotides on cross-stacking *oxrna2/xstk* and coaxial stacking interaction
opposite strands. Average sequence or sequence-dependent stacking and base-pairing strengths *oxrna2/coaxstk*, electrostatic Debye-Hueckel interaction *oxrna2/dh* as
are supported :ref:`(Sulc2) <Sulc32>`. Quasi-unique base-pairing between nucleotides can be achieved by using well as the hydrogen-bonding interaction *oxrna2/hbond* between
more complementary pairs of atom types like 5-8 and 6-7, 9-12 and 10-11, 13-16 and 14-15, etc. complementary pairs of nucleotides on opposite strands. Average sequence
This prevents the hybridization of in principle complementary bases within Ntypes/4 bases 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. up and down along the backbone.
The exact functional form of the pair styles is rather complex. The exact functional form of the pair styles is rather complex. The
The individual potentials consist of products of modulation factors, individual potentials consist of products of modulation factors, which
which themselves are constructed from a number of more basic potentials 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. (Morse, Lennard-Jones, harmonic angle and distance) as well as quadratic
We refer to :ref:`(Sulc1) <Sulc31>` and the original oxDNA publications :ref:`(Ouldridge-DPhil) <Ouldridge-DPhil3>` smoothing and modulation terms. We refer to :ref:`(Sulc1) <Sulc31>` and
and :ref:`(Ouldridge) <Ouldridge3>` for a detailed description of the oxRNA2 force field. the original oxDNA publications :ref:`(Ouldridge-DPhil)
<Ouldridge-DPhil3>` and :ref:`(Ouldridge) <Ouldridge3>` for a detailed
description of the oxRNA2 force field.
.. note:: .. note::
These pair styles have to be used together with the related oxDNA2 bond style These pair styles have to be used together with the related oxDNA2
*oxrna2/fene* for the connectivity of the phosphate backbone (see also documentation of bond style *oxrna2/fene* for the connectivity of the phosphate
:doc:`bond_style oxrna2/fene <bond_oxdna>`). Most of the coefficients backbone (see also documentation of :doc:`bond_style oxrna2/fene
in the above example have to be kept fixed and cannot be changed without reparameterizing the entire model. <bond_oxdna>`). Most of the coefficients in the above example have to
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), be kept fixed and cannot be changed without reparameterizing the
the first coefficient after *oxrna2/hbond* (seq=seqdep in the above example) and the three coefficients entire model. Exceptions are the first four coefficients after
after *oxrna2/dh* (T=0.1, rhos=0.5, qeff=1.02455 in the above example). When using a Langevin thermostat *oxrna2/stk* (seq=seqdep, T=0.1, xi=1.40206 and kappa=2.77 and
e.g. through :doc:`fix langevin <fix_langevin>` or :doc:`fix nve/dotc/langevin <fix_nve_dotc_langevin>` corresponding *real unit* equivalents in the above examples), the
the temperature coefficients have to be matched to the one used in the fix. 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:: .. note::
These pair styles have to be used with the *atom_style hybrid bond ellipsoid oxdna* These pair styles have to be used with the *atom_style hybrid bond
(see documentation of :doc:`atom_style <atom_style>`). The *atom_style oxdna* ellipsoid oxdna* (see documentation of :doc:`atom_style
stores the 3'-to-5' polarity of the nucleotide strand, which is set through <atom_style>`). The *atom_style oxdna* stores the 3'-to-5' polarity
the bond topology in the data file. The first (second) atom in a bond definition of the nucleotide strand, which is set through the bond topology in
is understood to point towards the 3'-end (5'-end) of the strand. 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/. Example input and data files for DNA duplexes can be found in
A simple python setup tool which creates single straight or helical DNA strands, ``examples/PACKAGES/cgdna/examples/oxDNA/`` and ``.../oxDNA2/``. A simple python
DNA duplexes or arrays of DNA duplexes can be found in examples/PACKAGES/cgdna/util/. 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 Please cite :ref:`(Henrich) <Henrich3>` in any publication that uses
this implementation. The article contains general information this implementation. The article contains general information on the
on the model, its implementation and performance as well as the structure of 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 the data and input file. The preprint version of the article can be
`here <PDF/CG-DNA.pdf>`_. found `here <PDF/CG-DNA.pdf>`_. Please cite also the relevant oxRNA2
Please cite also the relevant oxRNA2 publications publications :ref:`(Sulc1) <Sulc31>` and :ref:`(Sulc2) <Sulc32>`.
:ref:`(Sulc1) <Sulc31>` and :ref:`(Sulc2) <Sulc32>`.
---------- ----------
Potential file reading 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. For each pair style above the first non-modifiable argument can be a
Therefore the following command: 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 .. 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. will be interpreted as a request to read the corresponding hydrogen
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: 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 .. code-block:: LAMMPS
3 4 hbond <coefficients> 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 .. code-block:: LAMMPS
pair_style hybrid/overlay oxrna2/excv oxrna2/stk oxrna2/hbond oxrna2/xstk oxrna2/coaxstk oxrna2/dh 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/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/stk seqdep 0.1 1.40206 2.77 oxrna2_lj.cgdna
pair_coeff * * oxrna2/hbond seqdep oxrna2.lj pair_coeff * * oxrna2/hbond seqdep oxrna2_lj.cgdna
pair_coeff 1 4 oxrna2/hbond seqdep oxrna2.lj pair_coeff 1 4 oxrna2/hbond seqdep oxrna2_lj.cgdna
pair_coeff 2 3 oxrna2/hbond seqdep oxrna2.lj pair_coeff 2 3 oxrna2/hbond seqdep oxrna2_lj.cgdna
pair_coeff 3 4 oxrna2/hbond seqdep oxrna2.lj pair_coeff 3 4 oxrna2/hbond seqdep oxrna2_lj.cgdna
pair_coeff * * oxrna2/xstk oxrna2.lj pair_coeff * * oxrna2/xstk oxrna2_lj.cgdna
pair_coeff * * oxrna2/coaxstk oxrna2.lj pair_coeff * * oxrna2/coaxstk oxrna2_lj.cgdna
pair_coeff * * oxrna2/dh 0.1 0.5 1.02455 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 There are sample potential files for each unit style in the
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/. ``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 # oxDNA bond interactions - FENE backbone
bond_style oxdna/fene bond_style oxdna/fene
bond_coeff * oxdna.lj bond_coeff * oxdna_lj.cgdna
special_bonds lj 0 1 1 special_bonds lj 0 1 1
# oxDNA pair interactions # oxDNA pair interactions
pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk 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 oxdna.lj pair_coeff * * oxdna/stk seqav 0.1 1.3448 2.6568 oxdna_lj.cgdna
pair_coeff * * oxdna/hbond seqav oxdna.lj pair_coeff * * oxdna/hbond seqav oxdna_lj.cgdna
pair_coeff 1 4 oxdna/hbond seqav oxdna.lj pair_coeff 1 4 oxdna/hbond seqav oxdna_lj.cgdna
pair_coeff 2 3 oxdna/hbond seqav oxdna.lj pair_coeff 2 3 oxdna/hbond seqav oxdna_lj.cgdna
pair_coeff * * oxdna/xstk oxdna.lj pair_coeff * * oxdna/xstk oxdna_lj.cgdna
pair_coeff * * oxdna/coaxstk oxdna.lj pair_coeff * * oxdna/coaxstk oxdna_lj.cgdna
# NVE ensemble # NVE ensemble
fix 1 all nve/asphere fix 1 all nve/asphere

1
examples/PACKAGES/cgdna/examples/lj_units/oxDNA/potential_file/oxdna_lj.cgdna Symbolic link
View File

@ -0,0 +1 @@
../../../../../../../potentials/oxdna_lj.cgdna

18
examples/PACKAGES/cgdna/examples/lj_units/oxDNA2/potential_file/in.duplex1
View File

@ -27,19 +27,19 @@ group all type 1 4
# oxDNA2 bond interactions - FENE backbone # oxDNA2 bond interactions - FENE backbone
bond_style oxdna2/fene bond_style oxdna2/fene
bond_coeff * oxdna2.lj bond_coeff * oxdna2_lj.cgdna
special_bonds lj 0 1 1 special_bonds lj 0 1 1
# oxDNA2 pair interactions # oxDNA2 pair interactions
pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh 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/excv oxdna2_lj.cgdna
pair_coeff * * oxdna2/stk seqdep 0.1 1.3523 2.6717 oxdna2.lj pair_coeff * * oxdna2/stk seqdep 0.1 1.3523 2.6717 oxdna2_lj.cgdna
pair_coeff * * oxdna2/hbond seqdep oxdna2.lj pair_coeff * * oxdna2/hbond seqdep oxdna2_lj.cgdna
pair_coeff 1 4 oxdna2/hbond seqdep oxdna2.lj pair_coeff 1 4 oxdna2/hbond seqdep oxdna2_lj.cgdna
pair_coeff 2 3 oxdna2/hbond seqdep oxdna2.lj pair_coeff 2 3 oxdna2/hbond seqdep oxdna2_lj.cgdna
pair_coeff * * oxdna2/xstk oxdna2.lj pair_coeff * * oxdna2/xstk oxdna2_lj.cgdna
pair_coeff * * oxdna2/coaxstk oxdna2.lj pair_coeff * * oxdna2/coaxstk oxdna2_lj.cgdna
pair_coeff * * oxdna2/dh 0.1 0.5 oxdna2.lj pair_coeff * * oxdna2/dh 0.1 0.5 oxdna2_lj.cgdna
# NVE ensemble # NVE ensemble
fix 1 all nve/asphere fix 1 all nve/asphere

1
examples/PACKAGES/cgdna/examples/lj_units/oxDNA2/potential_file/oxdna2_lj.cgdna Symbolic link
View File

@ -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 # oxRNA2 bond interactions - FENE backbone
bond_style oxrna2/fene bond_style oxrna2/fene
bond_coeff * oxrna2.lj bond_coeff * oxrna2_lj.cgdna
special_bonds lj 0 1 1 special_bonds lj 0 1 1
# oxRNA2 pair interactions # oxRNA2 pair interactions
pair_style hybrid/overlay oxrna2/excv oxrna2/stk oxrna2/hbond oxrna2/xstk oxrna2/coaxstk oxrna2/dh 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/excv oxrna2_lj.cgdna
pair_coeff * * oxrna2/stk seqdep 0.1 1.40206 2.77 oxrna2.lj pair_coeff * * oxrna2/stk seqdep 0.1 1.40206 2.77 oxrna2_lj.cgdna
pair_coeff * * oxrna2/hbond seqdep oxrna2.lj pair_coeff * * oxrna2/hbond seqdep oxrna2_lj.cgdna
pair_coeff 1 4 oxrna2/hbond seqdep oxrna2.lj pair_coeff 1 4 oxrna2/hbond seqdep oxrna2_lj.cgdna
pair_coeff 2 3 oxrna2/hbond seqdep oxrna2.lj pair_coeff 2 3 oxrna2/hbond seqdep oxrna2_lj.cgdna
pair_coeff 3 4 oxrna2/hbond seqdep oxrna2.lj pair_coeff 3 4 oxrna2/hbond seqdep oxrna2_lj.cgdna
pair_coeff * * oxrna2/xstk oxrna2.lj pair_coeff * * oxrna2/xstk oxrna2_lj.cgdna
pair_coeff * * oxrna2/coaxstk oxrna2.lj pair_coeff * * oxrna2/coaxstk oxrna2_lj.cgdna
pair_coeff * * oxrna2/dh 0.1 0.5 oxrna2.lj pair_coeff * * oxrna2/dh 0.1 0.5 oxrna2_lj.cgdna
# NVE ensemble # NVE ensemble
fix 1 all nve/asphere fix 1 all nve/asphere

1
examples/PACKAGES/cgdna/examples/lj_units/oxRNA2/potential_file/oxrna2_lj.cgdna Symbolic link
View File

@ -0,0 +1 @@
../../../../../../../potentials/oxrna2_lj.cgdna

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

@ -27,18 +27,18 @@ group all type 1 4
# oxDNA bond interactions - FENE backbone # oxDNA bond interactions - FENE backbone
bond_style oxdna/fene bond_style oxdna/fene
bond_coeff * oxdna.real bond_coeff * oxdna_real.cgdna
special_bonds lj 0 1 1 special_bonds lj 0 1 1
# oxDNA pair interactions # oxDNA pair interactions
pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk
pair_coeff * * oxdna/excv oxdna.real pair_coeff * * oxdna/excv oxdna_real.cgdna
pair_coeff * * oxdna/stk seqav ${T} 8.01727944817084 0.005279604 oxdna.real pair_coeff * * oxdna/stk seqav ${T} 8.01727944817084 0.005279604 oxdna_real.cgdna
pair_coeff * * oxdna/hbond seqav oxdna.real pair_coeff * * oxdna/hbond seqav oxdna_real.cgdna
pair_coeff 1 4 oxdna/hbond seqav oxdna.real pair_coeff 1 4 oxdna/hbond seqav oxdna_real.cgdna
pair_coeff 2 3 oxdna/hbond seqav oxdna.real pair_coeff 2 3 oxdna/hbond seqav oxdna_real.cgdna
pair_coeff * * oxdna/xstk oxdna.real pair_coeff * * oxdna/xstk oxdna_real.cgdna
pair_coeff * * oxdna/coaxstk oxdna.real pair_coeff * * oxdna/coaxstk oxdna_real.cgdna
# NVE ensemble # NVE ensemble
fix 1 all nve/asphere fix 1 all nve/asphere

1
examples/PACKAGES/cgdna/examples/real_units/oxDNA/potential_file/oxdna_real.cgdna Symbolic link
View File

@ -0,0 +1 @@
../../../../../../../potentials/oxdna_real.cgdna

18
examples/PACKAGES/cgdna/examples/real_units/oxDNA2/potential_file/in.duplex1
View File

@ -28,19 +28,19 @@ group all type 1 4
# oxDNA2 bond interactions - FENE backbone # oxDNA2 bond interactions - FENE backbone
bond_style oxdna2/fene bond_style oxdna2/fene
bond_coeff * oxdna2.real bond_coeff * oxdna2_real.cgdna
special_bonds fene special_bonds fene
# oxDNA2 pair interactions # oxDNA2 pair interactions
pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh 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/excv oxdna2_real.cgdna
pair_coeff * * oxdna2/stk seqav 300.0 8.06199211612242 0.005309213 oxdna2.real pair_coeff * * oxdna2/stk seqav 300.0 8.06199211612242 0.005309213 oxdna2_real.cgdna
pair_coeff * * oxdna2/hbond seqav oxdna2.real pair_coeff * * oxdna2/hbond seqav oxdna2_real.cgdna
pair_coeff 1 4 oxdna2/hbond seqav oxdna2.real pair_coeff 1 4 oxdna2/hbond seqav oxdna2_real.cgdna
pair_coeff 2 3 oxdna2/hbond seqav oxdna2.real pair_coeff 2 3 oxdna2/hbond seqav oxdna2_real.cgdna
pair_coeff * * oxdna2/xstk oxdna2.real pair_coeff * * oxdna2/xstk oxdna2_real.cgdna
pair_coeff * * oxdna2/coaxstk oxdna2.real pair_coeff * * oxdna2/coaxstk oxdna2_real.cgdna
pair_coeff * * oxdna2/dh 300.0 0.5 oxdna2.real pair_coeff * * oxdna2/dh 300.0 0.5 oxdna2_real.cgdna
# NVE ensemble # 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 # oxRNA2 bond interactions - FENE backbone
bond_style oxrna2/fene bond_style oxrna2/fene
bond_coeff * oxrna2.real bond_coeff * oxrna2_real.cgdna
special_bonds lj 0 1 1 special_bonds lj 0 1 1
# oxRNA2 pair interactions # oxRNA2 pair interactions
pair_style hybrid/overlay oxrna2/excv oxrna2/stk oxrna2/hbond oxrna2/xstk oxrna2/coaxstk oxrna2/dh 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/excv oxrna2_real.cgdna
pair_coeff * * oxrna2/stk seqdep 300.0 8.35864576375849 0.005504556 oxrna2.real pair_coeff * * oxrna2/stk seqdep 300.0 8.35864576375849 0.005504556 oxrna2_real.cgdna
pair_coeff * * oxrna2/hbond seqdep oxrna2.real pair_coeff * * oxrna2/hbond seqdep oxrna2_real.cgdna
pair_coeff 1 4 oxrna2/hbond seqdep oxrna2.real pair_coeff 1 4 oxrna2/hbond seqdep oxrna2_real.cgdna
pair_coeff 2 3 oxrna2/hbond seqdep oxrna2.real pair_coeff 2 3 oxrna2/hbond seqdep oxrna2_real.cgdna
pair_coeff 3 4 oxrna2/hbond seqdep oxrna2.real pair_coeff 3 4 oxrna2/hbond seqdep oxrna2_real.cgdna
pair_coeff * * oxrna2/xstk oxrna2.real pair_coeff * * oxrna2/xstk oxrna2_real.cgdna
pair_coeff * * oxrna2/coaxstk oxrna2.real pair_coeff * * oxrna2/coaxstk oxrna2_real.cgdna
pair_coeff * * oxrna2/dh 300.0 0.5 oxrna2.real pair_coeff * * oxrna2/dh 300.0 0.5 oxrna2_real.cgdna
# NVE ensemble # NVE ensemble
fix 1 all nve/asphere fix 1 all nve/asphere

1
examples/PACKAGES/cgdna/examples/real_units/oxRNA2/potential_file/oxrna2_real.cgdna Symbolic link
View File

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

0
potentials/oxdna.lj → potentials/oxdna_lj.cgdna
View File

0
potentials/oxdna.real → potentials/oxdna_real.cgdna
View File

0
potentials/oxrna2.lj → potentials/oxrna2_lj.cgdna
View File

0
potentials/oxrna2.real → potentials/oxrna2_real.cgdna
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22
purge-workflows.py Normal file
View File

@ -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); T = utils::numeric(FLERR,arg[2],false,lmp);
rhos_dh_one = utils::numeric(FLERR,arg[3],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 if (comm->me == 0) { // read value from potential file
PotentialFileReader reader(lmp, arg[4], "oxdna potential", " (dh)"); PotentialFileReader reader(lmp, arg[4], "oxdna potential", " (dh)");
char * line; char * line;