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gmx-rama - Online in the Cloud

Run gmx-rama in OnWorks free hosting provider over Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

This is the command gmx-rama that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

PROGRAM:

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>
xvg plot formatting: xmgrace, xmgr, none

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