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GMX-MINDIST(1) GROMACS GMX-MINDIST(1) NAME gmx-mindist - Calculate the minimum distance between two groups SYNOPSIS gmx mindist [-f [_.xtc/.trr/..._]] [-s [_.tpr/.gro/..._]] [-n [_.ndx_]] [-od [_.xvg_]] [-on [_.xvg_]] [-o [_.out_]] [-ox [_.xtc/.trr/..._]] [-or [_.xvg_]] [-b _time_] [-e _time_] [-dt _time_] [-tu _enum_] [-[no]w] [-xvg _enum_] [-[no]matrix] [-[no]max] [-d _real_] [-[no]group] [-[no]pi] [-[no]split] [-ng _int_] [-[no]pbc] [-[no]respertime] [-[no]printresname] DESCRIPTION gmx mindist computes the distance between one group and a number of other groups. Both the minimum distance (between any pair of atoms from the respective groups) and the number of contacts within a given dis- tance are written to two separate output files. With the -group option a contact of an atom in another group with multiple atoms in the first group is counted as one contact instead of as multiple contacts. With -or, minimum distances to each residue in the first group are deter- mined and plotted as a function of residue number. With option -pi the minimum distance of a group to its periodic image is plotted. This is useful for checking if a protein has seen its peri- odic image during a simulation. Only one shift in each direction is considered, giving a total of 26 shifts. Note that periodicity informa- tion is required from the file supplied with with -s, either as a .tpr file or a .pdb file with CRYST1 fields. It also plots the maximum dis- tance within the group and the lengths of the three box vectors. Also gmx distance and gmx pairdist calculate distances. OPTIONS Options to specify input files: -f [<.xtc/.trr/^a|>] (traj.xtc) Trajectory: xtc trr cpt gro g96 pdb tng -s [<.tpr/.gro/^a|>] (topol.tpr) (Optional) Structure+mass(db): tpr gro g96 pdb brk ent -n [<.ndx>] (index.ndx) (Optional) Index file Options to specify output files: -od [<.xvg>] (mindist.xvg) xvgr/xmgr file -on [<.xvg>] (numcont.xvg) (Optional) xvgr/xmgr file -o [<.out>] (atm-pair.out) (Optional) Generic output file -ox [<.xtc/.trr/^a|>] (mindist.xtc) (Optional) Trajectory: xtc trr gro g96 pdb tng -or [<.xvg>] (mindistres.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) -tu <enum> (ps) Unit for time values: fs, ps, ns, us, ms, s -[no]w (no) View output .xvg, .xpm, .eps and .pdb files -xvg <enum> (xmgrace) xvg plot formatting: xmgrace, xmgr, none -[no]matrix (no) Calculate half a matrix of group-group distances -[no]max (no) Calculate maximum distance instead of minimum -d <real> (0.6) Distance for contacts -[no]group (no) Count contacts with multiple atoms in the first group as one -[no]pi (no) Calculate minimum distance with periodic images -[no]split (no) Split graph where time is zero -ng <int> (1) Number of secondary groups to compute distance to a central group -[no]pbc (yes) Take periodic boundary conditions into account -[no]respertime (no) When writing per-residue distances, write distance for each time point -[no]printresname (no) Write residue names SEE ALSO gmx(1) More information about GROMACS is available at <- http://www.gromacs.org/>. COPYRIGHT 2020, GROMACS development team 2020.4 Oct 06, 2020 GMX-MINDIST(1)
NAME | SYNOPSIS | DESCRIPTION | OPTIONS | SEE ALSO | COPYRIGHT
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