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GMX-SALTBR(1) GROMACS GMX-SALTBR(1)

NAME

gmx-saltbr - Compute salt bridges

SYNOPSIS

gmx saltbr [-f [<.xtc/.trr/...>]] [-s [<.tpr>]] [-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 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)
Time of first frame to read from trajectory (default unit ps)
-e <time> (0)
Time of last frame to read from trajectory (default unit ps)
-dt <time> (0)
Only use frame when t MOD dt = first time (default unit 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

gmx(1)

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

COPYRIGHT

2019, GROMACS development team
June 14, 2019 2019.3