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GMX-PAIRDIST(1) GROMACS GMX-PAIRDIST(1) NAME gmx-pairdist - Calculate pairwise distances between groups of positions SYNOPSIS gmx pairdist [-f [_.xtc/.trr/..._]] [-s [_.tpr/.gro/..._]] [-n [_.ndx_]] [-o [_.xvg_]] [-b _time_] [-e _time_] [-dt _time_] [-tu _enum_] [-fgroup _selection_] [-xvg _enum_] [-[no]rmpbc] [-[no]pbc] [-sf _file_] [-selrpos _enum_] [-seltype _enum_] [-cutoff _real_] [-type _enum_] [-refgrouping _enum_] [-selgrouping _enum_] [-ref _selection_] [-sel _selection_] DESCRIPTION gmx pairdist calculates pairwise distances between one reference selec- tion (given with -ref) and one or more other selections (given with -sel). It can calculate either the minimum distance (the default), or the maximum distance (with -type max). Distances to each selection provided with -sel are computed independently. By default, the global minimum/maximum distance is computed. To com- pute more distances (e.g., minimum distances to each residue in -ref), use -refgrouping and/or -selgrouping to specify how the positions within each selection should be grouped. Computed distances are written to the file specified with -o. If there are N groups in -ref and M groups in the first selection in -sel, then the output contains N*M columns for the first selection. The columns contain distances like this: r1-s1, r2-s1, a|, r1-s2, r2-s2, a|, where rn is the nath group in -ref and sn is the nath group in the other se- lection. The distances for the second selection comes as separate col- umns after the first selection, and so on. If some selections are dy- namic, only the selected positions are used in the computation but the same number of columns is always written out. If there are no posi- tions contributing to some group pair, then the cutoff value is written (see below). -cutoff sets a cutoff for the computed distances. If the result would contain a distance over the cutoff, the cutoff value is written to the output file instead. By default, no cutoff is used, but if you are not interested in values beyond a cutoff, or if you know that the minimum distance is smaller than a cutoff, you should set this option to allow the tool to use grid-based searching and be significantly faster. If you want to compute distances between fixed pairs, gmx distance may be a more suitable tool. OPTIONS Options to specify input files: -f [<.xtc/.trr/^a|>] (traj.xtc) (Optional) Input trajectory or single configuration: xtc trr cpt gro g96 pdb tng -s [<.tpr/.gro/^a|>] (topol.tpr) (Optional) Input structure: tpr gro g96 pdb brk ent -n [<.ndx>] (index.ndx) (Optional) Extra index groups Options to specify output files: -o [<.xvg>] (dist.xvg) Distances as function of time Other options: -b <time> (0) First frame (ps) to read from trajectory -e <time> (0) Last frame (ps) to read from trajectory -dt <time> (0) Only use frame if t MOD dt == first time (ps) -tu <enum> (ps) Unit for time values: fs, ps, ns, us, ms, s -fgroup <selection> Atoms stored in the trajectory file (if not set, assume first N atoms) -xvg <enum> (xmgrace) Plot formatting: none, xmgrace, xmgr -[no]rmpbc (yes) Make molecules whole for each frame -[no]pbc (yes) Use periodic boundary conditions for distance calculation -sf <file> Provide selections from files -selrpos <enum> (atom) Selection reference positions: atom, res_com, res_cog, mol_com, mol_cog, whole_res_com, whole_res_cog, whole_mol_com, whole_mol_cog, part_res_com, part_res_cog, part_mol_com, part_mol_cog, dyn_res_com, dyn_res_cog, dyn_mol_com, dyn_mol_cog -seltype <enum> (atom) Default selection output positions: atom, res_com, res_cog, mol_com, mol_cog, whole_res_com, whole_res_cog, whole_mol_com, whole_mol_cog, part_res_com, part_res_cog, part_mol_com, part_mol_cog, dyn_res_com, dyn_res_cog, dyn_mol_com, dyn_mol_cog -cutoff <real> (0) Maximum distance to consider -type <enum> (min) Type of distances to calculate: min, max -refgrouping <enum> (all) Grouping of -ref positions to compute the min/max over: all, res, mol, none -selgrouping <enum> (all) Grouping of -sel positions to compute the min/max over: all, res, mol, none -ref <selection> Reference positions to calculate distances from -sel <selection> Positions to calculate distances for 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-PAIRDIST(1)
NAME | SYNOPSIS | DESCRIPTION | OPTIONS | SEE ALSO | COPYRIGHT
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