Provided by: gromacs-data_2018.1-1_all bug


       gmx-check - Check and compare files


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


       gmx  check reads a trajectory (.tng, .trr or .xtc), an energy file (.edr) or an index file
       (.ndx) and prints out useful information about them.

       Option -c checks for presence of coordinates, velocities and box in the  file,  for  close
       contacts  (smaller  than  -vdwfac  and not bonded, i.e. not between -bonlo and -bonhi, 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.

       If an index file, is given its contents will be summarized.

       If both a trajectory and a .tpr file are given (with -s1) 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, gmx check provides a quick check for such problems.

       The  program  can  compare  two run input (.tpr) files when both -s1 and -s2 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  of  course  still  set  any  other
       tolerances through the options.Similarly a pair of trajectory files can be compared (using
       the -f2 option), or a pair of energy files (using the -e2 option).

       For free energy simulations the A and B state topology from one  run  input  file  can  be
       compared with options -s1 and -ab.

       In  case  the  -m flag is given a LaTeX file will be written consisting of a rough outline
       for a methods section for a paper.


       Options to specify input files:

       -f [<.xtc/.trr/…>] (traj.xtc) (Optional)
              Trajectory: xtc trr cpt gro g96 pdb tng

       -f2 [<.xtc/.trr/…>] (traj.xtc) (Optional)
              Trajectory: xtc trr cpt gro g96 pdb tng

       -s1 [<.tpr>] (top1.tpr) (Optional)
              Portable xdr run input file

       -s2 [<.tpr>] (top2.tpr) (Optional)
              Portable xdr run input file

       -c [<.tpr/.gro/…>] (topol.tpr) (Optional)
              Structure+mass(db): tpr gro g96 pdb brk ent

       -e [<.edr>] (ener.edr) (Optional)
              Energy file

       -e2 [<.edr>] (ener2.edr) (Optional)
              Energy file

       -n [<.ndx>] (index.ndx) (Optional)
              Index file

       Options to specify output files:

       -m [<.tex>] (doc.tex) (Optional)
              LaTeX file

       Other options:

       -vdwfac <real> (0.8)
              Fraction of sum of VdW radii used as warning cutoff

       -bonlo <real> (0.4)
              Min. fract. of sum of VdW radii for bonded atoms

       -bonhi <real> (0.7)
              Max. fract. of sum of VdW radii for bonded atoms

       -[no]rmsd (no)
              Print RMSD for x, v and f

       -tol <real> (0.001)
              Relative tolerance for comparing real values defined as 2*(a-b)/(|a|+|b|)

       -abstol <real> (0.001)
              Absolute tolerance, useful when sums are close to zero.

       -[no]ab (no)
              Compare the A and B topology from one file

       -lastener <string>
              Last energy term to compare (if not given all are tested). It makes sense to go  up
              until the Pressure.



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       2018, GROMACS development team