gmx-distance1
Calculate distances between pairs of positions
Usage
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>]
Overview
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: 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 |
-binw <real> (0.001)
|
Bin width for histogramming |
Releases
6 releases since Debian 8 (Jessie); the text changed 5 times.
-fgroup since Debian 9 (Stretch);
-select since Debian 9 (Stretch);
-sf since Debian 9 (Stretch).