gmx-mdmat - Calculate residue contact maps

       2025, GROMACS development team

2025.0                                            Feb 10, 2025                                      GMX-MDMAT(1)

gmxmdmat  makes  distance  matrices  consisting  of  the  smallest distance between residue pairs. With
       -frames, these distance matrices can be stored in order to see differences in  tertiary  structure  as  a
       function of time. If you choose your options unwisely, this may generate a large output file. By default,
       only  an  averaged  matrix  over the whole trajectory is output.  Also a count of the number of different
       atomic contacts between residues over the whole trajectory can be made.  The output can be processed with
       gmxxpm2ps to make a PostScript (tm) plot.

       gmx-mdmat - Calculate residue contact maps

       Options to specify input files:

       -f[<.xtc/.trr/...>](traj.xtc)
              Trajectory: xtctrrcptgrog96pdbtng-s[<.tpr/.gro/...>](topol.tpr)
              Structure+mass(db): tprgrog96pdb brk ent

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

       Options to specify output files:

       -mean[<.xpm>](dm.xpm)
              X PixMap compatible matrix file

       -frames[<.xpm>](dmf.xpm)(Optional)
              X PixMap compatible matrix file

       -no[<.xvg>](num.xvg)(Optional)
              xvgr/xmgr file

       Other options:

       -b<time>(0)
              Time of first frame to read from trajectory (default unit ps)

       -e<time>(0)
              Time of last frame to read from trajectory (default unit ps)

       -dt<time>(0)
              Only use frame when t MOD dt = first time (default unit ps)

       -xvg<enum>(xmgrace)
              xvg plot formatting: xmgrace, xmgr, none

       -t<real>(1.5)
              trunc distance

       -nlevels<int>(40)
              Discretize distance in this number of levels

gmx(1)

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

          gmx mdmat [-f[<.xtc/.trr/...>]] [-s[<.tpr/.gro/...>]] [-n[<.ndx>]]
                    [-mean[<.xpm>]] [-frames[<.xpm>]] [-no[<.xvg>]]
                    [-b<time>] [-e<time>] [-dt<time>] [-xvg<enum>]
                    [-t<real>] [-nlevels<int>]