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- jessie 5.0.2-1
gmx-saltbr(1) | GROMACS Manual | gmx-saltbr(1) |
NAME¶
gmx-saltbr - Compute salt bridgesSYNOPSIS¶
gmx saltbr [-f [<.xtc/.trr/...>]] [-s [<.tpr/.tpb/...>]][-nice <int>] [-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 and output files: -f [<.xtc/.trr/...>] (traj.xtc) (Input)Trajectory: xtc trr cpt trj gro g96 pdb tng -s [<.tpr/.tpb/...>] (topol.tpr) (Input)
Run input file: tpr tpb tpa Other options: -nice <int> (19)
Set the nicelevel -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¶
gromacs(7) More information about GROMACS is available at <http://www.gromacs.org/>.VERSION 5.0.2 |