Man page - gmx-distance(1)
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apt-get install gromacs-data
Manual
| 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 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 -len
- -binw <real> (0.001)
- Bin width for histogramming
SEE ALSO
gmx(1)
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| May 12, 2025 | 2025.2 |