Preparing coarse-grained runs¶
The coarse-grained run requires the molecule topology on the one hand and suitable potentials on the other. In this chapter, the generation of coarse-grained runs is described next, followed by a post-processing of the potential.
If the potential is of such a form that it allows direct fitting of a functional form, the section on post-processing can be skipped. Instead, a program of choice should be used to fit a functional form to the potential. Nevertheless, special attention should be paid to units (angles, bond lengths). The resulting curve can then be specified in the MD package used for simulation. However, most potentials don’t allow an easy processing of this kind and tabulated potentials have to be used.
Generating a topology file for a coarse-grained run¶
WARNING: This section describes experimental features. The exact names and options of the program might change in the near future. The section is specific to GROMACS support though a generalization for other MD packages is planned.
The mapping definition is close to a topology needed for a coarse
grained run. To avoid redundant work,
csg_gmxtopol can be used to automatically
generate a gromacs topology based on an atomistic reference system and a
At the current state,
csg_gmxtopol can only generate the topology for the first
molecule in the system. If more molecule types are present, a special
tpr file has to be prepared. The program can be executed by
csg_gmxtopol --top topol.tpr --cg map.xml --out cgtop
which will create a file
cgtop.top. This file includes the topology
for the first molecule including definitions for atoms, bonds, angles
and dihedrals. It can directly be used as a topology in GROMACS, however
the force field definitions (atom types, bond types, etc.) still have to
be added manually.
Post-processing of the potential¶
The VOTCA package provides a collection of scripts to handle potentials.
They can be modified, refined, integrated or inter- and extrapolated.
These scripts are the same ones as those used for iterative methods in
Iterative methods. Scripts are called by
csg_call. A complete
list of available scripts can be found in Scripts.
The post-processing roughly consists of the following steps (see further explanations below):
(manually) clipping poorly sampled (border) regions
resampling the potential in order to change the grid to the proper format ()
extrapolation of the potential at the borders ( table extrapolate)
exporting the table to xvg ( convert_potential gromacs)
Clipping of poorly sampled regions¶
Regions with an irregular distribution of samples should be deleted
first. This is simply done by editing the
.pot file and by deleting
Alternatively, manually check the range where the potential still looks
good and is not to noisy and set the flags in the potential file of the
bad parts by hand to
out of range). Those values will
later be extrapolated and overwritten.
Use the command
csg_resample --in table.pot --out table_resample.pot \ --grid min:step:max
to resample the potential given in file –
max with a grid spacing of
step steps. The result is written to
the file specified by
csg_resample allows the specification of
spline interpolation (
spfit), the calculation of derivatives
derivative) and comments (
comment). Check the help (
for further information.
It is important to note that the values
correspond to the minimum and maximum value in the input file, but to
the range of values the potential is desired to cover after
extrapolation. Therefore, values in \([ \min,\max ]\) that are not
covered in the file are automatically marked by a flag
out of range) for extrapolation in the next step.
The potential don’t have to start at 0, this is done by the export script (to xvg) automatically.
The following line
csg_call table extrapolate [options] table_resample.pot \ table_extrapolate.pot
calls the extrapolation procedure, which processes the range of values
csg_resample. The input file is
table_resample.pot created in the last
After resampling, all values in the potential file that should be used
as a basis for extrapolation are marked with an
i, while all values
that need extrapolation are marked by
o. The command above now
o values from the
i values in the file.
Available options include averaging over a certain number of points
avgpoints), changing the functional form (
function, default is
quadratic), extrapolating just the left or right region of the file
region) and setting the curvature (
table_extrapolate.pot of the extrapolation step can now
be used for the coarse-grained run. If GROMACS is used as a molecule
dynamics package, the potential has to be converted and exported to a
suitable GROMACS format as described in the final step.
Exporting the table¶
Finally, the table is exported to
xvg. The conversion procedure
requires a small xml file
table.xml as shown below:
<cg> <non-bonded> <name>XXX</name> <step>0.01</step> </non-bonded> <inverse> <gromacs> <pot_max>1e8</pot_max> <table_end>8.0</table_end> <table_bins>0.002</table_bins> </gromacs> </inverse> </cg>
<table_end> is the GROMACS
<pot_max> is just a number slightly smaller than the upper value of
single/ double precision. The value given in
corresponds to the
step value of
csg_resample -grid min:step:max.
xml file above, call
csg_call --options table.xml --ia-type non-bonded --ia-name XXX \ convert_potential gromacs table_extrapolate.pot table.xvg
to convert the extrapolated values in
table.xvg (The file will contain the GROMACS C12 parts only which are
stored in the sixth und seventh column, this can be changed by adding
–ia-type C6 option (for the fourth and fiveth column) or
–ia-type CB option (for the second and third column) after
compatibility with the GROMACS topology. See the GROMACS manual for
To obtain a bond table, run
csg_call --ia-type bond --ia-name XXX --options table.xml \ convert_potential gromacs table_extrapolate.pot table.xvg
It is also possible to use
dihedral as type as well,
but make to sure to have a
bonded section similar to the
non-bonded section above with the corresponding interaction name.
convert_potential gromacs will do the following steps:
Resampling of the potential from 0 (or -180 for dihedrals) to
table_end(or 180 for angles and dihedrals) with step size
table_bins. This is needed for gromacs the table must start with 0 or -180.
Extrapolate the left side (to 0 or -180) exponentially
Extrapolate the right side (to
table_endor 180) exponentially (or constant for non-bonded interactions)
Shift it so that the potential is zero at
table_endfor non-bonded interactions or zero at the minimum for bonded interaction
Calculate the force (assume periodicity for dihedral potentials)
Write to the format needed by gromacs
An example on non-bonded interactions¶
csg_call pot shift_nonbonded table.pot table.pot.refined csg_resample --grid 0.3:0.05:2 --in table.pot.refined \ --out table.pot.refined csg_call table extrapolate --function quadratic --region left \ table.pot.refined table.pot.refined csg_call table extrapolate --function constant --region right \ table.pot.refined table.pot.refined
Additionally to the two methods described above, namely (a) providing
the MD package directly with a functional form fitted with a program of
choice or (b) using
csg_call table extrapolate and
csg_call convert_potential, another method would be suitable. This
is integrating the force table as follows
# Integrate the table csg_call table integrate force.d minus_pot.d # multiply by -1 csg_call table linearop minus_pot.d pot.d -1 0