1GMX-CHECK(1)                        GROMACS                       GMX-CHECK(1)
2
3
4

NAME

6       gmx-check - Check and compare files
7

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>]
14

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.
19
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.
26
27       If an index file, is given its contents will be summarized.
28
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.
34
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).
43
44       For free energy simulations the A and B state topology from one run in‐
45       put file can be compared with options -s1 and -ab.
46

OPTIONS

48       Options to specify input files:
49
50       -f [<.xtc/.trr/...>] (traj.xtc) (Optional)
51              Trajectory: xtc trr cpt gro g96 pdb tng
52
53       -f2 [<.xtc/.trr/...>] (traj.xtc) (Optional)
54              Trajectory: xtc trr cpt gro g96 pdb tng
55
56       -s1 [<.tpr>] (top1.tpr) (Optional)
57              Portable xdr run input file
58
59       -s2 [<.tpr>] (top2.tpr) (Optional)
60              Portable xdr run input file
61
62       -c [<.tpr/.gro/...>] (topol.tpr) (Optional)
63              Structure+mass(db): tpr gro g96 pdb brk ent
64
65       -e [<.edr>] (ener.edr) (Optional)
66              Energy file
67
68       -e2 [<.edr>] (ener2.edr) (Optional)
69              Energy file
70
71       -n [<.ndx>] (index.ndx) (Optional)
72              Index file
73
74       Options to specify output files:
75
76       -m [<.tex>] (doc.tex) (Optional)
77              LaTeX file
78
79       Other options:
80
81       -vdwfac <real> (0.8)
82              Fraction of sum of VdW radii used as warning cutoff
83
84       -bonlo <real> (0.4)
85              Min. fract. of sum of VdW radii for bonded atoms
86
87       -bonhi <real> (0.7)
88              Max. fract. of sum of VdW radii for bonded atoms
89
90       -[no]rmsd (no)
91              Print RMSD for x, v and f
92
93       -tol <real> (0.001)
94              Relative  tolerance  for  comparing  real  values   defined   as
95              2*(a-b)/(|a|+|b|)
96
97       -abstol <real> (0.001)
98              Absolute tolerance, useful when sums are close to zero.
99
100       -[no]ab (no)
101              Compare the A and B topology from one file
102
103       -lastener <string>
104              Last  energy  term  to compare (if not given all are tested). It
105              makes sense to go up until the Pressure.
106

SEE ALSO

108       gmx(1)
109
110       More    information    about    GROMACS    is    available    at     <‐
111       http://www.gromacs.org/>.
112

114       2022, GROMACS development team
115
116
117
118
1192022.3                           Sep 02, 2022                     GMX-CHECK(1)
Impressum