gmx distance¶
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