gmx-saltbr man page

gmx-saltbr — Compute salt bridges


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


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 to specify input files:

-f [<.xtc/.trr/...>] (traj.xtc)

Trajectory: xtc trr cpt gro g96 pdb tng

-s [<.tpr>] (topol.tpr)

Portable xdr run input file

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 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


More information about GROMACS is available at <>.

Referenced By


Mar 13, 2017 2016.3 GROMACS