This is the command gmx-nmens 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-nmens - Generate an ensemble of structures from the normal modes
SYNOPSIS
gmx nmens [-v [<.trr/.cpt/...>]] [-e [<.xvg>]] [-s [<.tpr/.gro/...>]]
[-n [<.ndx>]] [-o [<.xtc/.trr/...>]] [-xvg <enum>]
[-temp <real>] [-seed <int>] [-num <int>] [-first <int>]
[-last <int>]
DESCRIPTION
gmx nmens generates an ensemble around an average structure in a subspace that is defined
by a set of normal modes (eigenvectors). The eigenvectors are assumed to be
mass-weighted. The position along each eigenvector is randomly taken from a Gaussian
distribution with variance kT/eigenvalue.
By default the starting eigenvector is set to 7, since the first six normal modes are the
translational and rotational degrees of freedom.
OPTIONS
Options to specify input files:
-v [<.trr/.cpt/...>] (eigenvec.trr)
Full precision trajectory: trr cpt tng
-e [<.xvg>] (eigenval.xvg)
xvgr/xmgr file
-s [<.tpr/.gro/...>] (topol.tpr)
Structure+mass(db): tpr gro g96 pdb brk ent
-n [<.ndx>] (index.ndx) (Optional)
Index file
Options to specify output files:
-o [<.xtc/.trr/...>] (ensemble.xtc)
Trajectory: xtc trr gro g96 pdb tng
Other options:
-xvg <enum>
xvg plot formatting: xmgrace, xmgr, none
-temp <real> (300)
Temperature in Kelvin
-seed <int> (-1)
Random seed, -1 generates a seed from time and pid
-num <int> (100)
Number of structures to generate
-first <int> (7)
First eigenvector to use (-1 is select)
-last <int> (-1)
Last eigenvector to use (-1 is till the last)
Use gmx-nmens online using onworks.net services
