NAME
grompp - makes a run input file
VERSION 4.0.1
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 -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 calls a preprocessor to resolve includes, macros etcetera. By
default we use the cpp in your path. To specify a different
macro-preprocessor (e.g. m4) or alternative location you can put a line
in your parameter file specifying the path to that program. Specifying
-pp will get the pre-processed topology file written out.
If your system does not have a c-preprocessor, you can still use
grompp, but you do not have access to the features from the cpp.
Command line options to the c-preprocessor can be given in the .mdp
file. See your local manual (man cpp).
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. 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 have exact restarts when using pressure and/or Nose-Hoover
temperature coupling. For an exact restart do not forget to turn off
velocity generation and turn on unconstrained starting when constraints
are present in the system. If you want to continue a crashed run, it
is easier to use tpbconv.
Using the -morse option grompp can convert the harmonic bonds in your
topology to morse potentials. This makes it possible to break bonds.
For this option to work you need an extra file in your $GMXLIB with
dissociation energy. Use the -debug option to get more information on
the workings of this option (look for MORSE in the grompp.log file
using less or something like that).
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 make notice 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). Finally, you can see the
contents of the run input file with the gmxdump program.
FILES
-f grompp.mdp Input, Opt.
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 tpb tpa
-r conf.gro Input, Opt.
Structure file: gro g96 pdb tpr tpb tpa
-rb conf.gro Input, Opt.
Structure file: gro g96 pdb tpr tpb tpa
-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: edr ene
OTHER OPTIONS
-[no]hno
Print help info and quit
-nice int 0
Set the nicelevel
-[no]vyes
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
-[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/>.
Thu 16 Oct 2008 grompp(1)