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)