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.TH "GMX-DUMP" "1" "Feb 15, 2019" "2019.1" "GROMACS"
.SH NAME
gmx-dump \- Make binary files human readable
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.SH SYNOPSIS
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.sp
.nf
.ft C
gmx dump [\fB\-s\fP \fI[<.tpr>]\fP] [\fB\-f\fP \fI[<.xtc/.trr/...>]\fP] [\fB\-e\fP \fI[<.edr>]\fP]
         [\fB\-cp\fP \fI[<.cpt>]\fP] [\fB\-p\fP \fI[<.top>]\fP] [\fB\-mtx\fP \fI[<.mtx>]\fP] [\fB\-om\fP \fI[<.mdp>]\fP]
         [\fB\-[no]nr\fP] [\fB\-[no]param\fP] [\fB\-[no]sys\fP] [\fB\-[no]orgir\fP]
.ft P
.fi
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.SH DESCRIPTION
.sp
\fBgmx dump\fP reads a run input file (\&.tpr),
a trajectory (\&.trr/\&.xtc/\fB/tng\fP), an energy
file (\&.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
problems.
.sp
The program can also preprocess a topology to help finding problems.
Note that currently setting \fBGMXLIB\fP is the only way to customize
directories used for searching include files.
.SH OPTIONS
.sp
Options to specify input files:
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.TP
.B \fB\-s\fP [<.tpr>] (topol.tpr) (Optional)
Portable xdr run input file
.TP
.B \fB\-f\fP [<.xtc/.trr/…>] (traj.xtc) (Optional)
Trajectory: xtc trr cpt gro g96 pdb tng
.TP
.B \fB\-e\fP [<.edr>] (ener.edr) (Optional)
Energy file
.TP
.B \fB\-cp\fP [<.cpt>] (state.cpt) (Optional)
Checkpoint file
.TP
.B \fB\-p\fP [<.top>] (topol.top) (Optional)
Topology file
.TP
.B \fB\-mtx\fP [<.mtx>] (hessian.mtx) (Optional)
Hessian matrix
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.sp
Options to specify output files:
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.TP
.B \fB\-om\fP [<.mdp>] (grompp.mdp) (Optional)
grompp input file with MD parameters
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.sp
Other options:
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.TP
.B \fB\-[no]nr\fP  (yes)
Show index numbers in output (leaving them out makes comparison easier, but creates a useless topology)
.TP
.B \fB\-[no]param\fP  (no)
Show parameters for each bonded interaction (for comparing dumps, it is useful to combine this with \-nonr)
.TP
.B \fB\-[no]sys\fP  (no)
List the atoms and bonded interactions for the whole system instead of for each molecule type
.TP
.B \fB\-[no]orgir\fP  (no)
Show input parameters from tpr as they were written by the version that produced the file, instead of how the current version reads them
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.SH KNOWN ISSUES
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.IP \(bu 2
Position restraint output from \-sys \-s is broken
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.SH SEE ALSO
.sp
\fBgmx(1)\fP
.sp
More information about GROMACS is available at <\fI\%http://www.gromacs.org/\fP>.
.SH COPYRIGHT
2019, GROMACS development team
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