1gmxcheck(1)               GROMACS suite, VERSION 4.5               gmxcheck(1)
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NAME

6       gmxcheck - checks and compares files
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8       VERSION 4.5
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SYNOPSIS

11       gmxcheck  -f  traj.xtc  -f2  traj.xtc  -s1  top1.tpr  -s2  top2.tpr  -c
12       topol.tpr -e ener.edr -e2 ener2.edr  -n  index.ndx  -m  doc.tex  -[no]h
13       -[no]version  -nice  int -vdwfac real -bonlo real -bonhi real -[no]rmsd
14       -tol real -abstol real -[no]ab -lastener string
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DESCRIPTION

17       gmxcheck reads a trajectory ( .trj,  .trr or  .xtc), an energy  file  (
18       .ene  or  .edr) or an index file ( .ndx) and prints out useful informa‐
19       tion about them.
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22       Option  -c checks for presence of coordinates, velocities  and  box  in
23       the  file,  for  close  contacts (smaller than  -vdwfac and not bonded,
24       i.e. not between  -bonlo and  -bonhi, all relative to the sum  of  both
25       Van  der  Waals radii) and atoms outside the box (these may occur often
26       and are no problem). If velocities are present, an  estimated  tempera‐
27       ture will be calculated from them.
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30       If an index file, is given its contents will be summarized.
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33       If  both  a trajectory and a tpr file are given (with  -s1) the program
34       will check whether the bond lengths defined in the tpr file are  indeed
35       correct  in  the trajectory. If not you may have non-matching files due
36       to e.g. deshuffling or due to problems with virtual sites.  With  these
37       flags, gmxcheck provides a quick check for such problems.
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40       The  program  can  compare  two run input ( .tpr,  .tpb or  .tpa) files
41       when both  -s1 and  -s2 are supplied.  Similarly a pair  of  trajectory
42       files  can  be  compared  (using  the  -f2 option), or a pair of energy
43       files (using the  -e2 option).
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46       For free energy simulations the A and B state  topology  from  one  run
47       input file can be compared with options  -s1 and  -ab.
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50       In  case  the  -m flag is given a LaTeX file will be written consisting
51       of a rough outline for a methods section for a paper.
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FILES

54       -f traj.xtc Input, Opt.
55        Trajectory: xtc trr trj gro g96 pdb cpt
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57       -f2 traj.xtc Input, Opt.
58        Trajectory: xtc trr trj gro g96 pdb cpt
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60       -s1 top1.tpr Input, Opt.
61        Run input file: tpr tpb tpa
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63       -s2 top2.tpr Input, Opt.
64        Run input file: tpr tpb tpa
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66       -c topol.tpr Input, Opt.
67        Structure+mass(db): tpr tpb tpa gro g96 pdb
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69       -e ener.edr Input, Opt.
70        Energy file
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72       -e2 ener2.edr Input, Opt.
73        Energy file
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75       -n index.ndx Input, Opt.
76        Index file
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78       -m doc.tex Output, Opt.
79        LaTeX file
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OTHER OPTIONS

83       -[no]hno
84        Print help info and quit
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86       -[no]versionno
87        Print version info and quit
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89       -nice int 0
90        Set the nicelevel
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92       -vdwfac real 0.8
93        Fraction of sum of VdW radii used as warning cutoff
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95       -bonlo real 0.4
96        Min. fract. of sum of VdW radii for bonded atoms
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98       -bonhi real 0.7
99        Max. fract. of sum of VdW radii for bonded atoms
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101       -[no]rmsdno
102        Print RMSD for x, v and f
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104       -tol real 0.001
105        Relative   tolerance   for   comparing   real   values   defined    as
106       2*(a-b)/(|a|+|b|)
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108       -abstol real 0.001
109        Absolute tolerance, useful when sums are close to zero.
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111       -[no]abno
112        Compare the A and B topology from one file
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114       -lastener string
115        Last  energy  term  to compare (if not given all are tested). It makes
116       sense to go up until the Pressure.
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SEE ALSO

120       gromacs(7)
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122       More  information  about  GROMACS  is  available  at   <http://www.gro‐
123       macs.org/>.
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127                                Thu 26 Aug 2010                    gmxcheck(1)