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)- 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)
-[no]w
(no)- View output .xvg, .xpm, .eps and .pdb files
-xvg
<enum> (xmgrace)- xvg plot formatting: xmgrace, xmgr, none