gmx pairdist [-f [<.xtc/.trr/...>]] [-s [<.tpr/.gro/...>]] [-n [<.ndx>]] [-o [<.xvg>]] [-b <time>] [-e <time>] [-dt <time>] [-tu <enum>] [-fgroup <selection>] [-xvg <enum>] [-[no]rmpbc] [-[no]pbc] [-sf <file>] [-selrpos <enum>] [-seltype <enum>] [-cutoff <real>] [-type <enum>] [-refgrouping <enum>] [-selgrouping <enum>] [-ref <selection>] [-sel <selection>]
gmx pairdist calculates pairwise distances between one reference
selection (given with
-ref) and one or more other selections
-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
to specify how the positions within each selection should be
Computed distances are written to the file specified with
If there are N groups in
-ref and M groups in the first
-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
-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 to specify input files:
-f[<.xtc/.trr/…>] (traj.xtc) (Optional)
-s[<.tpr/.gro/…>] (topol.tpr) (Optional)
-n[<.ndx>] (index.ndx) (Optional)
Extra index groups
Options to specify output files:
Distances as function of time
First frame (ps) to read from trajectory
Last frame (ps) to read from trajectory
Only use frame if t MOD dt == first time (ps)
Unit for time values: fs, ps, ns, us, ms, s
Atoms stored in the trajectory file (if not set, assume first N atoms)
Plot formatting: xmgrace, xmgr, none
Make molecules whole for each frame
Use periodic boundary conditions for distance calculation
Provide selections from files
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
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
Maximum distance to consider
Type of distances to calculate: min, max
Grouping of -ref positions to compute the min/max over: all, res, mol, none
Grouping of -sel positions to compute the min/max over: all, res, mol, none
Reference positions to calculate distances from
Positions to calculate distances for