NAME
gmx-rama - Compute Ramachandran plots
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
SEE ALSO
More information about GROMACS is available at <http://www.gromacs.org/>.
COPYRIGHT
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