gmx saltbr¶
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)- 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)