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gmx-distance - Online in the Cloud

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This is the command gmx-distance that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

PROGRAM:

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>] [-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

-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

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