gmx rama¶

Synopsis¶

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

-f [<.xtc/.trr/…>] (traj.xtc): Trajectory: xtc trr cpt gro g96 pdb tng
-s [<.tpr>] (topol.tpr): Portable xdr run input file

Options to specify output files:

-o [<.xvg>] (rama.xvg): xvgr/xmgr file

Other options:

-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>: xvg plot formatting: xmgrace, xmgr, none