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.TH "GMX-CHECK" "1" "Dec 14, 2018" "2019-rc1" "GROMACS"
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.SH NAME
gmx-check \- Check and compare files
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.SH SYNOPSIS
.INDENT 0.0
.INDENT 3.5
.sp
.nf
.ft C
gmx check [\fB\-f\fP \fI[<.xtc/.trr/...>]\fP] [\fB\-f2\fP \fI[<.xtc/.trr/...>]\fP] [\fB\-s1\fP \fI[<.tpr>]\fP]
          [\fB\-s2\fP \fI[<.tpr>]\fP] [\fB\-c\fP \fI[<.tpr/.gro/...>]\fP] [\fB\-e\fP \fI[<.edr>]\fP]
          [\fB\-e2\fP \fI[<.edr>]\fP] [\fB\-n\fP \fI[<.ndx>]\fP] [\fB\-m\fP \fI[<.tex>]\fP] [\fB\-vdwfac\fP \fI<real>\fP]
          [\fB\-bonlo\fP \fI<real>\fP] [\fB\-bonhi\fP \fI<real>\fP] [\fB\-[no]rmsd\fP] [\fB\-tol\fP \fI<real>\fP]
          [\fB\-abstol\fP \fI<real>\fP] [\fB\-[no]ab\fP] [\fB\-lastener\fP \fI<string>\fP]
.ft P
.fi
.UNINDENT
.UNINDENT
.SH DESCRIPTION
.sp
\fBgmx check\fP reads a trajectory (\&.tng, \&.trr or
\&.xtc), an energy file (\&.edr)
or an index file (\&.ndx)
and prints out useful information about them.
.sp
Option \fB\-c\fP checks for presence of coordinates,
velocities and box in the file, for close contacts (smaller than
\fB\-vdwfac\fP and not bonded, i.e. not between \fB\-bonlo\fP
and \fB\-bonhi\fP, all relative to the sum of both Van der Waals
radii) and atoms outside the box (these may occur often and are
no problem). If velocities are present, an estimated temperature
will be calculated from them.
.sp
If an index file, is given its contents will be summarized.
.sp
If both a trajectory and a \&.tpr file are given (with \fB\-s1\fP)
the program will check whether the bond lengths defined in the tpr
file are indeed correct in the trajectory. If not you may have
non\-matching files due to e.g. deshuffling or due to problems with
virtual sites. With these flags, \fBgmx check\fP provides a quick check for such problems.
.sp
The program can compare two run input (\&.tpr)
files
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when both \fB\-s1\fP and \fB\-s2\fP are supplied. When comparing
run input files this way, the default relative tolerance is reduced
to 0.000001 and the absolute tolerance set to zero to find any differences
not due to minor compiler optimization differences, although you can
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of course still set any other tolerances through the options.
Similarly a pair of trajectory files can be compared (using the \fB\-f2\fP
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option), or a pair of energy files (using the \fB\-e2\fP option).
.sp
For free energy simulations the A and B state topology from one
run input file can be compared with options \fB\-s1\fP and \fB\-ab\fP\&.
.SH OPTIONS
.sp
Options to specify input files:
.INDENT 0.0
.TP
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.B \fB\-f\fP [<.xtc/.trr/…>] (traj.xtc) (Optional)
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Trajectory: xtc trr cpt gro g96 pdb tng
.TP
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.B \fB\-f2\fP [<.xtc/.trr/…>] (traj.xtc) (Optional)
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Trajectory: xtc trr cpt gro g96 pdb tng
.TP
.B \fB\-s1\fP [<.tpr>] (top1.tpr) (Optional)
Portable xdr run input file
.TP
.B \fB\-s2\fP [<.tpr>] (top2.tpr) (Optional)
Portable xdr run input file
.TP
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.B \fB\-c\fP [<.tpr/.gro/…>] (topol.tpr) (Optional)
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Structure+mass(db): tpr gro g96 pdb brk ent
.TP
.B \fB\-e\fP [<.edr>] (ener.edr) (Optional)
Energy file
.TP
.B \fB\-e2\fP [<.edr>] (ener2.edr) (Optional)
Energy file
.TP
.B \fB\-n\fP [<.ndx>] (index.ndx) (Optional)
Index file
.UNINDENT
.sp
Options to specify output files:
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.TP
.B \fB\-m\fP [<.tex>] (doc.tex) (Optional)
LaTeX file
.UNINDENT
.sp
Other options:
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.TP
.B \fB\-vdwfac\fP <real> (0.8)
Fraction of sum of VdW radii used as warning cutoff
.TP
.B \fB\-bonlo\fP <real> (0.4)
Min. fract. of sum of VdW radii for bonded atoms
.TP
.B \fB\-bonhi\fP <real> (0.7)
Max. fract. of sum of VdW radii for bonded atoms
.TP
.B \fB\-[no]rmsd\fP  (no)
Print RMSD for x, v and f
.TP
.B \fB\-tol\fP <real> (0.001)
Relative tolerance for comparing real values defined as 2*(a\-b)/(|a|+|b|)
.TP
.B \fB\-abstol\fP <real> (0.001)
Absolute tolerance, useful when sums are close to zero.
.TP
.B \fB\-[no]ab\fP  (no)
Compare the A and B topology from one file
.TP
.B \fB\-lastener\fP <string>
Last energy term to compare (if not given all are tested). It makes sense to go up until the Pressure.
.UNINDENT
.SH SEE ALSO
.sp
\fBgmx(1)\fP
.sp
More information about GROMACS is available at <\fI\%http://www.gromacs.org/\fP>.
.SH COPYRIGHT
153
2018, GROMACS development team
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