gmx-rama man page

gmx-rama ā€” Compute Ramachandran plots


gmx rama [-f [<.xtc/.trr/...>]] [-s [<.tpr>]] [-o [<.xvg>]] [-b <time>]
         [-e <time>] [-dt <time>] [-[no]w] [-xvg <enum>]


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 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> (xmgrace)

xvg plot formatting: xmgrace, xmgr, none

See Also


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Referenced By


Sep 15, 2017 2016.4 GROMACS