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GMX-DISTANCE(1) GROMACS GMX-DISTANCE(1) NAME gmx-distance - Calculate distances between pairs of positions SYNOPSIS gmx distance [-f [<.xtc/.trr/...>]] [-s [<.tpr/.gro/...>]] [-n [<.ndx>]] [-oav [<.xvg>]] [-oall [<.xvg>]] [-oxyz [<.xvg>]] [-oh [<.xvg>]] [-oallstat [<.xvg>]] [-b <time>] [-e <time>] [-dt <time>] [-tu <enum>] [-fgroup <selection>] [-xvg <enum>] [-[no]rmpbc] [-[no]pbc] [-sf <file>] [-selrpos <enum>] [-seltype <enum>] [-select <selection>] [-len <real>] [-tol <real>] [-binw <real>] DESCRIPTION gmx distance calculates distances between pairs of positions as a func- tion of time. Each selection specifies an independent set of distances to calculate. Each selection should consist of pairs of positions, and the distances are computed between positions 1-2, 3-4, etc. -oav writes the average distance as a function of time for each selec- tion. -oall writes all the individual distances. -oxyz does the same, but the x, y, and z components of the distance are written instead of the norm. -oh writes a histogram of the distances for each selection. The location of the histogram is set with -len and -tol. Bin width is set with -binw. -oallstat writes out the average and standard devia- tion for each individual distance, calculated over the frames. Note that gmx distance calculates distances between fixed pairs (1-2, 3-4, etc.) within a single selection. To calculate distances between two selections, including minimum, maximum, and pairwise distances, use gmx pairdist. OPTIONS Options to specify input files: -f [<.xtc/.trr/...>] (traj.xtc) (Optional) Input trajectory or single configuration: xtc trr cpt gro g96 pdb tng -s [<.tpr/.gro/...>] (topol.tpr) (Optional) Input structure: tpr gro g96 pdb brk ent -n [<.ndx>] (index.ndx) (Optional) Extra index groups Options to specify output files: -oav [<.xvg>] (distave.xvg) (Optional) Average distances as function of time -oall [<.xvg>] (dist.xvg) (Optional) All distances as function of time -oxyz [<.xvg>] (distxyz.xvg) (Optional) Distance components as function of time -oh [<.xvg>] (disthist.xvg) (Optional) Histogram of the distances -oallstat [<.xvg>] (diststat.xvg) (Optional) Statistics for individual distances 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: xmgrace, xmgr, none -[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 -select <selection> Position pairs to calculate distances for -len <real> (0.1) Mean distance for histogramming -tol <real> (1) Width of full distribution as fraction of -len -binw <real> (0.001) Bin width for histogramming SEE ALSO gmx(1) More information about GROMACS is available at <- http://www.gromacs.org/>. COPYRIGHT 2025, GROMACS development team 2025.0 Feb 10, 2025 GMX-DISTANCE(1)
NAME | SYNOPSIS | DESCRIPTION | OPTIONS | SEE ALSO | COPYRIGHT
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