DragonFly On-Line Manual Pages

gmx-saltbr(1)                   GROMACS Manual                   gmx-saltbr(1)

NAME
       gmx-saltbr - Compute salt bridges

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

DESCRIPTION
       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)

SEE ALSO
       gromacs(7)

       More information about GROMACS is available at
       <http://www.gromacs.org/>.

VERSION 5.0.6                                                    gmx-saltbr(1)