gmxdump(1) GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c gmxdump(1)NAME
gmxdump - makes binary files human readable
VERSION 4.5.4-dev-20110404-bc5695c
SYNOPSIS
gmxdump -s topol.tpr -f traj.xtc -e ener.edr -cp state.cpt -p topol.top -mtx hessian.mtx -om grompp.mdp -[no]h -[no]version -nice int
-[no]nr -[no]sys
DESCRIPTION
gmxdump reads a run input file ( .tpa/ .tpr/ .tpb), a trajectory ( .trj/ .trr/ .xtc), an energy file ( .ene/ .edr), or a checkpoint file (
.cpt) and prints that to standard output in a readable format. This program is essential for checking your run input file in case of prob-
lems.
The program can also preprocess a topology to help finding problems. Note that currently setting GMXLIB is the only way to customize
directories used for searching include files.
FILES -s topol.tpr Input, Opt.
Run input file: tpr tpb tpa
-f traj.xtc Input, Opt.
Trajectory: xtc trr trj gro g96 pdb cpt
-e ener.edr Input, Opt.
Energy file
-cp state.cpt Input, Opt.
Checkpoint file
-p topol.top Input, Opt.
Topology file
-mtx hessian.mtx Input, Opt.
Hessian matrix
-om grompp.mdp Output, Opt.
grompp input file with MD parameters
OTHER OPTIONS
-[no]hno
Print help info and quit
-[no]versionno
Print version info and quit
-nice int 0
Set the nicelevel
-[no]nryes
Show index numbers in output (leaving them out makes comparison easier, but creates a useless topology)
-[no]sysno
List the atoms and bonded interactions for the whole system instead of for each molecule type
SEE ALSO gromacs(7)
More information about GROMACS is available at <http://www.gromacs.org/>.
Mon 4 Apr 2011 gmxdump(1)
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g_principal(1) GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c g_principal(1)NAME
g_principal - calculates axes of inertia for a group of atoms
VERSION 4.5.4-dev-20110404-bc5695c
SYNOPSIS
g_principal -f traj.xtc -s topol.tpr -n index.ndx -a1 axis1.dat -a2 axis2.dat -a3 axis3.dat -om moi.dat -[no]h -[no]version -nice int -b
time -e time -dt time -tu enum -[no]w -[no]foo
DESCRIPTION
g_principal calculates the three principal axes of inertia for a group of atoms.
FILES -f traj.xtc Input
Trajectory: xtc trr trj gro g96 pdb cpt
-s topol.tpr Input
Structure+mass(db): tpr tpb tpa gro g96 pdb
-n index.ndx Input, Opt.
Index file
-a1 axis1.dat Output
Generic data file
-a2 axis2.dat Output
Generic data file
-a3 axis3.dat Output
Generic data file
-om moi.dat Output
Generic data file
OTHER OPTIONS
-[no]hno
Print help info and quit
-[no]versionno
Print version info and quit
-nice int 19
Set the nicelevel
-b time 0
First frame (ps) to read from trajectory
-e time 0
Last frame (ps) to read from trajectory
-dt time 0
Only use frame when t MOD dt = first time (ps)
-tu enum ps
Time unit: fs, ps, ns, us, ms or s
-[no]wno
View output .xvg, .xpm, .eps and .pdb files
-[no]foono
Dummy option to avoid empty array
SEE ALSO gromacs(7)
More information about GROMACS is available at <http://www.gromacs.org/>.
Mon 4 Apr 2011 g_principal(1)
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