gmx-check - Check and compare files

       2025, GROMACS development team

2025.0                                            Feb 10, 2025                                      GMX-CHECK(1)

gmxcheck  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, gmxcheck 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.

       gmx-check - Check and compare files

       Options to specify input files:

       -f[<.xtc/.trr/...>](traj.xtc)(Optional)
              Trajectory: xtctrrcptgrog96pdbtng-f2[<.xtc/.trr/...>](traj.xtc)(Optional)
              Trajectory: xtctrrcptgrog96pdbtng-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): tprgrog96pdb 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.

gmx(1)

       More information about GROMACS is available at <http://www.gromacs.org/>.

          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>]