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

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:

Trajectory: xtc trr cpt gro g96 pdb tng
Portable xdr run input file

Other options:

Time of first frame to read from trajectory (default unit ps)
Time of last frame to read from trajectory (default unit ps)
Only use frame when t MOD dt = first time (default unit ps)
Groups that are never closer than this distance are not plotted
-[no]sep (no)
Use separate files for each interaction (may be MANY)

gmx(1)

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2023, GROMACS development team

February 3, 2023 2022.5