.TH gmx-saltbr 1 "" "VERSION 5.0.2" "GROMACS Manual"
.SH NAME
gmx-saltbr \- Compute salt bridges

.SH SYNOPSIS
gmx saltbr [\-f [<.xtc/.trr/...>]] [\-s [<.tpr/.tpb/...>]]
           [\-nice <int>] [\-b <time>] [\-e <time>] [\-dt <time>]
           [\-t <real>] [\-[no]sep]

.SH DESCRIPTION
\fBgmx saltbr\fR 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, \fBmin\-min.xvg\fR, \fBplus\-min.xvg\fR and \fBplus\-plus.xvg\fR, or files for every individual ion pair if the \fB\-sep\fR option is selected. In this case, files are named as \fBsb\-(Resname)(Resnr)\-(Atomnr)\fR. There may be \fBmany\fR such files.

.SH OPTIONS
Options to specify input and output files:

.BI "\-f" " [<.xtc/.trr/...>] (traj.xtc) (Input)"
    Trajectory: xtc trr cpt trj gro g96 pdb tng

.BI "\-s" " [<.tpr/.tpb/...>] (topol.tpr) (Input)"
    Run input file: tpr tpb tpa


Other options:

.BI "\-nice" " <int> (19)"
    Set the nicelevel

.BI "\-b" " <time> (0)"
    First frame (ps) to read from trajectory

.BI "\-e" " <time> (0)"
    Last frame (ps) to read from trajectory

.BI "\-dt" " <time> (0)"
    Only use frame when t MOD dt = first time (ps)

.BI "\-t" " <real> (1000)"
    Groups that are never closer than this distance are not plotted

.BI "\-[no]sep" "  (no)"
    Use separate files for each interaction (may be MANY)


.SH SEE ALSO
.BR gromacs(7)

More information about \fBGROMACS\fR is available at <\fIhttp://www.gromacs.org/\fR>.