g_saltbr1
Compute salt bridges
Part of gmx-saltbr(1).
Usage
gmx saltbr
[-f
[<.xtc/.trr/ ...
>]]
[-s
[<.tpr/.tpb/ ...
>]]
[-nice
<int>]
[-b
<time>]
[-e
<time>]
[-dt
<time>]
[-t
<real>]
[-
[no]
sep]
Overview
gmx saltbr plots the distance between all combination of charged groups as a function of time. The groups are combined in different ways. A minimum distance can be given (i.e. a cut-off), such that groups that are never closer than that distance will not be plotted.
Output will be in a number of fixed filenames, min-min.xvg, plus-min.xvg and plus-plus.xvg, or files for every individual ion pair if the -sep option is selected. In this case, files are named as sb-(Resname)(Resnr)-(Atomnr). There may be many such files.
Options
Options to specify input and output files:
-f [<.xtc/.trr/...>] (traj.xtc) (Input)
Trajectory: xtc trr cpt trj gro g96 pdb tng
-s [<.tpr/.tpb/...>] (topol.tpr) (Input)
Run input file: tpr tpb tpa
Other options:
-nice <int> (19)
Set the nicelevel
-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 when t MOD dt = first time (ps)
-t <real> (1000)
Groups that are never closer than this distance are not plotted
-[no]sep (no)
Use separate files for each interaction (may be MANY)
Releases
5 releases since Debian 4.0 (Etch); the text changed 4 times.