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 op- tion 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 h5md -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 2026, GROMACS development team 2026.3 Jun 25, 2026 GMX-SALTBR(1)
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