1 .TH gmxcheck 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
3 gmxcheck - checks and compares files
5 .B VERSION 4.5.4-dev-20110404-bc5695c
9 .BI "\-f2" " traj.xtc "
10 .BI "\-s1" " top1.tpr "
11 .BI "\-s2" " top2.tpr "
12 .BI "\-c" " topol.tpr "
13 .BI "\-e" " ener.edr "
14 .BI "\-e2" " ener2.edr "
15 .BI "\-n" " index.ndx "
18 .BI "\-[no]version" ""
20 .BI "\-vdwfac" " real "
21 .BI "\-bonlo" " real "
22 .BI "\-bonhi" " real "
25 .BI "\-abstol" " real "
27 .BI "\-lastener" " string "
29 \&\fB gmxcheck\fR reads a trajectory (\fB .trj\fR, \fB .trr\fR or
30 \&\fB .xtc\fR), an energy file (\fB .ene\fR or \fB .edr\fR)
31 \&or an index file (\fB .ndx\fR)
32 \&and prints out useful information about them.
35 \&Option \fB \-c\fR checks for presence of coordinates,
36 \&velocities and box in the file, for close contacts (smaller than
37 \&\fB \-vdwfac\fR and not bonded, i.e. not between \fB \-bonlo\fR
38 \&and \fB \-bonhi\fR, all relative to the sum of both Van der Waals
39 \&radii) and atoms outside the box (these may occur often and are
40 \&no problem). If velocities are present, an estimated temperature
41 \&will be calculated from them.
44 \&If an index file, is given its contents will be summarized.
47 \&If both a trajectory and a \fB .tpr\fR file are given (with \fB \-s1\fR)
48 \&the program will check whether the bond lengths defined in the tpr
49 \&file are indeed correct in the trajectory. If not you may have
50 \&non\-matching files due to e.g. deshuffling or due to problems with
51 \&virtual sites. With these flags, \fB gmxcheck\fR provides a quick check for such problems.
54 \&The program can compare two run input (\fB .tpr\fR, \fB .tpb\fR or
56 \&when both \fB \-s1\fR and \fB \-s2\fR are supplied.
57 \&Similarly a pair of trajectory files can be compared (using the \fB \-f2\fR
58 \&option), or a pair of energy files (using the \fB \-e2\fR option).
61 \&For free energy simulations the A and B state topology from one
62 \&run input file can be compared with options \fB \-s1\fR and \fB \-ab\fR.
65 \&In case the \fB \-m\fR flag is given a LaTeX file will be written
66 \&consisting of a rough outline for a methods section for a paper.
70 Trajectory: xtc trr trj gro g96 pdb cpt
72 .BI "\-f2" " traj.xtc"
74 Trajectory: xtc trr trj gro g96 pdb cpt
76 .BI "\-s1" " top1.tpr"
78 Run input file: tpr tpb tpa
80 .BI "\-s2" " top2.tpr"
82 Run input file: tpr tpb tpa
84 .BI "\-c" " topol.tpr"
86 Structure+mass(db): tpr tpb tpa gro g96 pdb
92 .BI "\-e2" " ener2.edr"
96 .BI "\-n" " index.ndx"
106 Print help info and quit
108 .BI "\-[no]version" "no "
109 Print version info and quit
111 .BI "\-nice" " int" " 0"
114 .BI "\-vdwfac" " real" " 0.8 "
115 Fraction of sum of VdW radii used as warning cutoff
117 .BI "\-bonlo" " real" " 0.4 "
118 Min. fract. of sum of VdW radii for bonded atoms
120 .BI "\-bonhi" " real" " 0.7 "
121 Max. fract. of sum of VdW radii for bonded atoms
123 .BI "\-[no]rmsd" "no "
124 Print RMSD for x, v and f
126 .BI "\-tol" " real" " 0.001 "
127 Relative tolerance for comparing real values defined as 2*(a\-b)/(|a|+|b|)
129 .BI "\-abstol" " real" " 0.001 "
130 Absolute tolerance, useful when sums are close to zero.
133 Compare the A and B topology from one file
135 .BI "\-lastener" " string" " "
136 Last energy term to compare (if not given all are tested). It makes sense to go up until the Pressure.
141 More information about \fBGROMACS\fR is available at <\fIhttp://www.gromacs.org/\fR>.