This is the command gmx-pairdist 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-pairdist - Calculate pairwise distances between groups of positions
SYNOPSIS
gmx pairdist [-f [<.xtc/.trr/...>]] [-s [<.tpr/.gro/...>]] [-n [<.ndx>]]
[-o [<.xvg>]] [-b <time>] [-e <time>] [-dt <time>]
[-tu <enum>] [-xvg <enum>] [-[no]rmpbc] [-[no]pbc]
[-sf <file>] [-selrpos <enum>] [-seltype <enum>]
[-cutoff <real>] [-type <enum>] [-refgrouping <enum>]
[-selgrouping <enum>] [-ref <selection>]
[-sel <selection>]
DESCRIPTION
gmx pairdist calculates pairwise distances between one reference selection (given with
-ref) and one or more other selections (given with -sel). It can calculate either the
minimum distance (the default), or the maximum distance (with -type max). Distances to
each selection provided with -sel are computed independently.
By default, the global minimum/maximum distance is computed. To compute more distances
(e.g., minimum distances to each residue in -ref), use -refgrouping and/or -selgrouping to
specify how the positions within each selection should be grouped.
Computed distances are written to the file specified with -o. If there are N groups in
-ref and M groups in the first selection in -sel, then the output contains N*M columns for
the first selection. The columns contain distances like this: r1-s1, r2-s1, ..., r1-s2,
r2-s2, ..., where rn is the n'th group in -ref and sn is the n'th group in the other
selection. The distances for the second selection comes as separate columns after the
first selection, and so on. If some selections are dynamic, only the selected positions
are used in the computation but the same number of columns is always written out. If
there are no positions contributing to some group pair, then the cutoff value is written
(see below).
-cutoff sets a cutoff for the computed distances. If the result would contain a distance
over the cutoff, the cutoff value is written to the output file instead. By default, no
cutoff is used, but if you are not interested in values beyond a cutoff, or if you know
that the minimum distance is smaller than a cutoff, you should set this option to allow
the tool to use grid-based searching and be significantly faster.
If you want to compute distances between fixed pairs, gmx distance may be a more suitable
tool.
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:
-o [<.xvg>] (dist.xvg)
Distances as function of time
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
-cutoff <real> (0)
Maximum distance to consider
-type <enum> (min)
Type of distances to calculate: min, max
-refgrouping <enum> (all)
Grouping of -ref positions to compute the min/max over: all, res, mol, none
-selgrouping <enum> (all)
Grouping of -sel positions to compute the min/max over: all, res, mol, none
-ref <selection>
Reference positions to calculate distances from
-sel <selection>
Positions to calculate distances for
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