gmx distance
Main Table of Contents VERSION 5.0

Synopsis

gmx distance [-f [<.xtc/.trr/...>]] [-s [<.tpr/.tpb/...>]] [-n [<.ndx>]]
             [-oav [<.xvg>]] [-oall [<.xvg>]] [-oxyz [<.xvg>]] [-oh [<.xvg>]]
             [-oallstat [<.xvg>]] [-b

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.

Options

Options to specify input and output files:

-f [<.xtc/.trr/...>] (traj.xtc) (Input, Optional)
Input trajectory or single configuration: xtc trr cpt trj gro g96 pdb tng
-s [<.tpr/.tpb/...>] (topol.tpr) (Input, Optional)
Input structure: tpr tpb tpa gro g96 pdb brk ent
-n [<.ndx>] (index.ndx) (Input, Optional)
Extra index groups
-oav [<.xvg>] (distave.xvg) (Output, Optional)
Average distances as function of time
-oall [<.xvg>] (dist.xvg) (Output, Optional)
All distances as function of time
-oxyz [<.xvg>] (distxyz.xvg) (Output, Optional)
Distance components as function of time
-oh [<.xvg>] (disthist.xvg) (Output, Optional)
Histogram of the distances
-oallstat [<.xvg>] (diststat.xvg) (Output, 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
-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
-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

http://www.gromacs.org