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

6       gmx-saltbr - Compute salt bridges
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SYNOPSIS

9          gmx saltbr [-f [<.xtc/.trr/...>]] [-s [<.tpr>]] [-b <time>] [-e <time>]
10                     [-dt <time>] [-t <real>] [-[no]sep]
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DESCRIPTION

13       gmx saltbr plots the distance between all combination of charged groups
14       as a function of time. The groups are combined in  different  ways.   A
15       minimum  distance  can be given (i.e. a cut-off), such that groups that
16       are never closer than that distance will not be plotted.
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18       Output  will  be  in  a  number  of   fixed   filenames,   min-min.xvg,
19       plus-min.xvg  and plus-plus.xvg, or files for every individual ion pair
20       if the -sep option is selected.  In  this  case,  files  are  named  as
21       sb-(Resname)(Resnr)-(Atomnr).  There may be many such files.
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OPTIONS

24       Options to specify input files:
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26       -f [<.xtc/.trr/…>] (traj.xtc)
27              Trajectory: xtc trr cpt gro g96 pdb tng
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29       -s [<.tpr>] (topol.tpr)
30              Portable xdr run input file
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32       Other options:
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34       -b <time> (0)
35              Time of first frame to read from trajectory (default unit ps)
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37       -e <time> (0)
38              Time of last frame to read from trajectory (default unit ps)
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40       -dt <time> (0)
41              Only use frame when t MOD dt = first time (default unit ps)
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43       -t <real> (1000)
44              Groups that are never closer than this distance are not plotted
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46       -[no]sep (no)
47              Use separate files for each interaction (may be MANY)
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SEE ALSO

50       gmx(1)
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52       More     information    about    GROMACS    is    available    at    <‐
53       http://www.gromacs.org/>.
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56       2019, GROMACS development team
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612019.2                           Apr 16, 2019                    GMX-SALTBR(1)
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