NAME¶
grompp - makes a run input file
VERSION 4.5.4-dev-20110404-bc5695c
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 -[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
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/>.