Provided by: gromacs-data_4.6.5-1build1_all 
NAME
grompp - makes a run input file
VERSION 4.6.5
SYNOPSIS
grompp -f grompp.mdp -po mdout.mdp -c conf.gro -r conf.gro -rb conf.gro -n index.ndx -p
topol.top -pp processed.top -o topol.tpr -t traj.trr -e ener.edr -ref rotref.trr -[no]h
-[no]version -nice int -[no]v -time real -[no]rmvsbds -maxwarn int -[no]zero -[no]renum
DESCRIPTION
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. grompp also reads parameters for the 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.
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.
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.
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 tpbconv is more convenient than grompp. You then supply the old checkpoint
file directly to mdrun with -cpi. If you wish to change the ensemble or things like
output frequency, then supplying the checkpoint file to grompp with -t along with a new
.mdp file with -f is the recommended procedure.
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 grompp has read. If in doubt, you can start
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 gmxdump program. gmxcheck can be used to compare the contents of two run input
files.
The -maxwarn option can be used to override warnings printed by 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.
FILES
-f grompp.mdp Input
grompp input file with MD parameters
-po mdout.mdp Output
grompp input file with MD parameters
-c conf.gro Input
Structure file: gro g96 pdb tpr etc.
-r conf.gro Input, Opt.
Structure file: gro g96 pdb tpr etc.
-rb conf.gro Input, Opt.
Structure file: gro g96 pdb tpr etc.
-n index.ndx Input, Opt.
Index file
-p topol.top Input
Topology file
-pp processed.top Output, Opt.
Topology file
-o topol.tpr Output
Run input file: tpr tpb tpa
-t traj.trr Input, Opt.
Full precision trajectory: trr trj cpt
-e ener.edr Input, Opt.
Energy file
-ref rotref.trr In/Out, Opt.
Full precision trajectory: trr trj cpt
OTHER OPTIONS
-[no]hno
Print help info and quit
-[no]versionno
Print version info and quit
-nice int 0
Set the nicelevel
-[no]vno
Be loud and noisy
-time real -1
Take frame at or first after this time.
-[no]rmvsbdsyes
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]zerono
Set parameters for bonded interactions without defaults to zero instead of generating an
error
-[no]renumyes
Renumber atomtypes and minimize number of atomtypes
SEE ALSO
gromacs(7)
More information about GROMACS is available at <http://www.gromacs.org/>.
Mon 2 Dec 2013 grompp(1)