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
More information about GROMACS is available at <- http://www.gromacs.org/>.
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2020, GROMACS development team