Compute ramachandran plots
gmx rama [-f [<.xtc/.trr/...>]] [-s [<.tpr/.tpb/...>]] [-o [<.xvg>]]
[-nice <int>] [-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 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
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