SYNOPSIS

gmx rama [-f [<.xtc/.trr/...>]] [-s [<.tpr/.tpb/...>]] [-o [<.xvg>]]

         [-nice <int>] [-b <time>] [-e <time>] [-dt <time>] [-[no]w]
         [-xvg <enum>]

DESCRIPTION

gmx rama selects the phi/psi dihedral combinations from your topology file and computes these as a function of time. Using simple Unix tools such as grep you can select out specific residues.

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

-o [<.xvg>] (rama.xvg) (Output)

    xvgr/xmgr file

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)

-[no]w (no)

    View output .xvg, .xpm, .eps and .pdb files

-xvg <enum> (xmgrace)

    xvg plot formatting: xmgrace, xmgr, none

RELATED TO gmx-rama…

gromacs(7)

More information about GROMACS is available at <http://www.gromacs.org/>.