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This is the command gmx-saltbr that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

PROGRAM:

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)
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)

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