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 function 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 selection. -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 deviation 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: 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

-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)

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