gmx-grompp(1) GROMACS Manual gmx-grompp(1)NAMEgmx-grompp - Make a run input file
SYNOPSIS
gmx grompp [-f [<.mdp>]] [-po [<.mdp>]] [-c [<.gro/.g96/...>]]
[-r [<.gro/.g96/...>]] [-rb [<.gro/.g96/...>]]
[-n [<.ndx>]] [-p [<.top>]] [-pp [<.top>]]
[-o [<.tpr/.tpb/...>]] [-t [<.trr/.cpt/...>]]
[-e [<.edr>]] [-imd [<.gro>]] [-ref [<.trr/.cpt/...>]]
[-nice <int>] [-[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 infor‐
mation about molecule types and the number of molecules, the preproces‐
sor copies each molecule as needed. There is no limitation on the num‐
ber of molecule types. Bonds and bond-angles can be converted into con‐
straints, separately for hydrogens and heavy atoms. Then a coordinate
file is read and velocities can be generated from a Maxwellian distri‐
bution 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 VARI‐
ABLE 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 vari‐
ables.
gmx grompp can be used to restart simulations (preserving continuity)
by supplying just a checkpoint file with -t. However, for simply chang‐
ing 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 ensem‐
ble 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 recom‐
mended 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 vir‐
tual 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 harm‐
less, but usually they are not. The user is advised to carefully inter‐
pret the output messages before attempting to bypass them with this
option.
OPTIONS
Options to specify input and output files:
-f [<.mdp>] (grompp.mdp) (Input)
grompp input file with MD parameters
-po [<.mdp>] (mdout.mdp) (Output)
grompp input file with MD parameters
-c [<.gro/.g96/...>] (conf.gro) (Input)
Structure file: gro g96 pdb brk ent esp tpr tpb tpa
-r [<.gro/.g96/...>] (conf.gro) (Input, Optional)
Structure file: gro g96 pdb brk ent esp tpr tpb tpa
-rb [<.gro/.g96/...>] (conf.gro) (Input, Optional)
Structure file: gro g96 pdb brk ent esp tpr tpb tpa
-n [<.ndx>] (index.ndx) (Input, Optional)
Index file
-p [<.top>] (topol.top) (Input)
Topology file
-pp [<.top>] (processed.top) (Output, Optional)
Topology file
-o [<.tpr/.tpb/...>] (topol.tpr) (Output)
Run input file: tpr tpb tpa
-t [<.trr/.cpt/...>] (traj.trr) (Input, Optional)
Full precision trajectory: trr cpt trj tng
-e [<.edr>] (ener.edr) (Input, Optional)
Energy file
-imd [<.gro>] (imdgroup.gro) (Output, Optional)
Coordinate file in Gromos-87 format
-ref [<.trr/.cpt/...>] (rotref.trr) (Input/Output, Optional)
Full precision trajectory: trr cpt trj tng
Other options:
-nice <int> (0)
Set the nicelevel
-[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
SEE ALSOgromacs(7)
More information about GROMACS is available at <http://www.gro‐
macs.org/>.
VERSION 5.0.6gmx-grompp(1)
