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gmx-rama - Compute Ramachandran plots

GMX-RAMA(1) GROMACS GMX-RAMA(1)

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)
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

gmx(1)
 
More information about GROMACS is available at < http://www.gromacs.org/>. 2017, GROMACS development team
September 15, 2017 2016.4