.. _gmx saltbr: gmx saltbr ========== Synopsis -------- .. parsed-literal:: gmx saltbr [:strong:`-f` :emphasis:`[<.xtc/.trr/...>]`] [:strong:`-s` :emphasis:`[<.tpr>]`] [:strong:`-b` :emphasis:`<time>`] [:strong:`-e` :emphasis:`<time>`] [:strong:`-dt` :emphasis:`<time>`] [:strong:`-t` :emphasis:`<real>`] [:strong:`-[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: :ref:`xtc` :ref:`trr` :ref:`cpt` :ref:`gro` :ref:`g96` :ref:`pdb` :ref:`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) .. only:: man See also -------- :manpage:`gmx(1)` More information about |Gromacs| is available at <http://www.gromacs.org/>.