This is the command gmx-grompp that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
PROGRAM:
NAME
gmx-grompp - Make a run input file
SYNOPSIS
gmx grompp [-f [<.mdp>]] [-c [<.gro/.g96/...>]] [-r [<.gro/.g96/...>]]
[-rb [<.gro/.g96/...>]] [-n [<.ndx>]] [-p [<.top>]]
[-t [<.trr/.cpt/...>]] [-e [<.edr>]]
[-ref [<.trr/.cpt/...>]] [-po [<.mdp>]] [-pp [<.top>]]
[-o [<.tpr>]] [-imd [<.gro>]] [-[no]v] [-time <real>]
[-[no]rmvsbds] [-maxwarn <int>] [-[no]zero] [-[no]renum]
DESCRIPTION
gmx grompp (the gromacs preprocessor) reads a molecular topology file, checks the validity
of the file, expands the topology from a molecular description to an atomic description.
The topology file contains information about molecule types and the number of molecules,
the preprocessor copies each molecule as needed. There is no limitation on the number of
molecule types. Bonds and bond-angles can be converted into constraints, separately for
hydrogens and heavy atoms. Then a coordinate file is read and velocities can be generated
from a Maxwellian distribution if requested. gmx grompp also reads parameters for gmx
mdrun (eg. number of MD steps, time step, cut-off), and others such as NEMD parameters,
which are corrected so that the net acceleration is zero. Eventually a binary file is
produced that can serve as the sole input file for the MD program.
gmx grompp uses the atom names from the topology file. The atom names in the coordinate
file (option -c) are only read to generate warnings when they do not match the atom names
in the topology. Note that the atom names are irrelevant for the simulation as only the
atom types are used for generating interaction parameters.
gmx grompp uses a built-in preprocessor to resolve includes, macros, etc. The preprocessor
supports the following keywords:
#ifdef VARIABLE
#ifndef VARIABLE
#else
#endif
#define VARIABLE
#undef VARIABLE
#include "filename"
#include <filename>
The functioning of these statements in your topology may be modulated by using the
following two flags in your .mdp file:
define = -DVARIABLE1 -DVARIABLE2
include = -I/home/john/doe
For further information a C-programming textbook may help you out. Specifying the -pp
flag will get the pre-processed topology file written out so that you can verify its
contents.
When using position restraints a file with restraint coordinates can be supplied with -r,
otherwise restraining will be done with respect to the conformation from the -c option.
For free energy calculation the the coordinates for the B topology can be supplied with
-rb, otherwise they will be equal to those of the A topology.
Starting coordinates can be read from trajectory with -t. The last frame with coordinates
and velocities will be read, unless the -time option is used. Only if this information is
absent will the coordinates in the -c file be used. Note that these velocities will not
be used when gen_vel = yes in your .mdp file. An energy file can be supplied with -e to
read Nose-Hoover and/or Parrinello-Rahman coupling variables.
gmx grompp can be used to restart simulations (preserving continuity) by supplying just a
checkpoint file with -t. However, for simply changing the number of run steps to extend a
run, using gmx convert-tpr is more convenient than gmx grompp. You then supply the old
checkpoint file directly to gmx mdrun with -cpi. If you wish to change the ensemble or
things like output frequency, then supplying the checkpoint file to gmx grompp with -t
along with a new .mdp file with -f is the recommended procedure. Actually preserving the
ensemble (if possible) still requires passing the checkpoint file to gmx mdrun -cpi.
By default, all bonded interactions which have constant energy due to virtual site
constructions will be removed. If this constant energy is not zero, this will result in a
shift in the total energy. All bonded interactions can be kept by turning off -rmvsbds.
Additionally, all constraints for distances which will be constant anyway because of
virtual site constructions will be removed. If any constraints remain which involve
virtual sites, a fatal error will result.
To verify your run input file, please take note of all warnings on the screen, and correct
where necessary. Do also look at the contents of the mdout.mdp file; this contains comment
lines, as well as the input that gmx grompp has read. If in doubt, you can start gmx
grompp with the -debug option which will give you more information in a file called
grompp.log (along with real debug info). You can see the contents of the run input file
with the gmx dump program. gmx check can be used to compare the contents of two run input
files.
The -maxwarn option can be used to override warnings printed by gmx grompp that otherwise
halt output. In some cases, warnings are harmless, but usually they are not. The user is
advised to carefully interpret the output messages before attempting to bypass them with
this option.
OPTIONS
Options to specify input files:
-f [<.mdp>] (grompp.mdp)
grompp input file with MD parameters
-c [<.gro/.g96/...>] (conf.gro)
Structure file: gro g96 pdb brk ent esp tpr
-r [<.gro/.g96/...>] (conf.gro) (Optional)
Structure file: gro g96 pdb brk ent esp tpr
-rb [<.gro/.g96/...>] (conf.gro) (Optional)
Structure file: gro g96 pdb brk ent esp tpr
-n [<.ndx>] (index.ndx) (Optional)
Index file
-p [<.top>] (topol.top)
Topology file
-t [<.trr/.cpt/...>] (traj.trr) (Optional)
Full precision trajectory: trr cpt tng
-e [<.edr>] (ener.edr) (Optional)
Energy file
Options to specify input/output files:
-ref [<.trr/.cpt/...>] (rotref.trr) (Optional)
Full precision trajectory: trr cpt tng
Options to specify output files:
-po [<.mdp>] (mdout.mdp)
grompp input file with MD parameters
-pp [<.top>] (processed.top) (Optional)
Topology file
-o [<.tpr>] (topol.tpr)
Portable xdr run input file
-imd [<.gro>] (imdgroup.gro) (Optional)
Coordinate file in Gromos-87 format
Other options:
-[no]v (no)
Be loud and noisy
-time <real> (-1)
Take frame at or first after this time.
-[no]rmvsbds (yes)
Remove constant bonded interactions with virtual sites
-maxwarn <int> (0)
Number of allowed warnings during input processing. Not for normal use and may
generate unstable systems
-[no]zero (no)
Set parameters for bonded interactions without defaults to zero instead of
generating an error
-[no]renum (yes)
Renumber atomtypes and minimize number of atomtypes
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