1GMX-CHECK(1)                        GROMACS                       GMX-CHECK(1)
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NAME

6       gmx-check - Check and compare files
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SYNOPSIS

9          gmx check [-f [<.xtc/.trr/...>]] [-f2 [<.xtc/.trr/...>]] [-s1 [<.tpr>]]
10                    [-s2 [<.tpr>]] [-c [<.tpr/.gro/...>]] [-e [<.edr>]]
11                    [-e2 [<.edr>]] [-n [<.ndx>]] [-m [<.tex>]] [-vdwfac <real>]
12                    [-bonlo <real>] [-bonhi <real>] [-[no]rmsd] [-tol <real>]
13                    [-abstol <real>] [-[no]ab] [-lastener <string>]
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DESCRIPTION

16       gmx  check  reads  a  trajectory  (.tng,  .trr or .xtc), an energy file
17       (.edr) or an index file (.ndx) and prints out useful information  about
18       them.
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20       Option -c checks for presence of coordinates, velocities and box in the
21       file, for close contacts (smaller than -vdwfac and not bonded, i.e. not
22       between  -bonlo  and  -bonhi,  all  relative to the sum of both Van der
23       Waals radii) and atoms outside the box (these may occur often  and  are
24       no  problem).  If velocities are present, an estimated temperature will
25       be calculated from them.
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27       If an index file, is given its contents will be summarized.
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29       If both a trajectory and a .tpr file are given (with -s1)  the  program
30       will  check whether the bond lengths defined in the tpr file are indeed
31       correct in the trajectory. If not you may have non-matching  files  due
32       to  e.g.  deshuffling or due to problems with virtual sites. With these
33       flags, gmx check provides a quick check for such problems.
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35       The program can compare two run input (.tpr) files when  both  -s1  and
36       -s2  are supplied. When comparing run input files this way, the default
37       relative tolerance is reduced to 0.000001 and  the  absolute  tolerance
38       set to zero to find any differences not due to minor compiler optimiza‐
39       tion differences, although you can of course still set any other toler‐
40       ances  through  the options.Similarly a pair of trajectory files can be
41       compared (using the -f2 option), or a pair of energy files  (using  the
42       -e2 option).
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44       For  free  energy  simulations  the A and B state topology from one run
45       input file can be compared with options -s1 and -ab.
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47       In case the -m flag is given a LaTeX file will be written consisting of
48       a rough outline for a methods section for a paper.
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OPTIONS

51       Options to specify input files:
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53       -f [<.xtc/.trr/…>] (traj.xtc) (Optional)
54              Trajectory: xtc trr cpt gro g96 pdb tng
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56       -f2 [<.xtc/.trr/…>] (traj.xtc) (Optional)
57              Trajectory: xtc trr cpt gro g96 pdb tng
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59       -s1 [<.tpr>] (top1.tpr) (Optional)
60              Portable xdr run input file
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62       -s2 [<.tpr>] (top2.tpr) (Optional)
63              Portable xdr run input file
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65       -c [<.tpr/.gro/…>] (topol.tpr) (Optional)
66              Structure+mass(db): tpr gro g96 pdb brk ent
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68       -e [<.edr>] (ener.edr) (Optional)
69              Energy file
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71       -e2 [<.edr>] (ener2.edr) (Optional)
72              Energy file
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74       -n [<.ndx>] (index.ndx) (Optional)
75              Index file
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77       Options to specify output files:
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79       -m [<.tex>] (doc.tex) (Optional)
80              LaTeX file
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82       Other options:
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84       -vdwfac <real> (0.8)
85              Fraction of sum of VdW radii used as warning cutoff
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87       -bonlo <real> (0.4)
88              Min. fract. of sum of VdW radii for bonded atoms
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90       -bonhi <real> (0.7)
91              Max. fract. of sum of VdW radii for bonded atoms
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93       -[no]rmsd (no)
94              Print RMSD for x, v and f
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96       -tol <real> (0.001)
97              Relative   tolerance   for  comparing  real  values  defined  as
98              2*(a-b)/(|a|+|b|)
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100       -abstol <real> (0.001)
101              Absolute tolerance, useful when sums are close to zero.
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103       -[no]ab (no)
104              Compare the A and B topology from one file
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106       -lastener <string>
107              Last energy term to compare (if not given all  are  tested).  It
108              makes sense to go up until the Pressure.
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SEE ALSO

111       gmx(1)
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113       More     information    about    GROMACS    is    available    at    <‐
114       http://www.gromacs.org/>.
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117       2019, GROMACS development team
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1222018.7                           May 29, 2019                     GMX-CHECK(1)
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