gmx-nmens(1) GROMACS Manual gmx-nmens(1)NAMEgmx-nmens - Generate an ensemble of structures from the normal modes
SYNOPSIS
gmx nmens [-v [<.trr/.cpt/...>]] [-e [<.xvg>]]
[-s [<.tpr/.tpb/...>]] [-n [<.ndx>]] [-o [<.xtc/.trr/...>]]
[-nice <int>] [-xvg <enum>] [-temp <real>] [-seed <int>]
[-num <int>] [-first <int>] [-last <int>]
DESCRIPTION
gmx nmens generates an ensemble around an average structure in a sub‐
space 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 vari‐
ance 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 and output files:
-v [<.trr/.cpt/...>] (eigenvec.trr) (Input)
Full precision trajectory: trr cpt trj tng
-e [<.xvg>] (eigenval.xvg) (Input)
xvgr/xmgr file
-s [<.tpr/.tpb/...>] (topol.tpr) (Input)
Structure+mass(db): tpr tpb tpa gro g96 pdb brk ent
-n [<.ndx>] (index.ndx) (Input, Optional)
Index file
-o [<.xtc/.trr/...>] (ensemble.xtc) (Output)
Trajectory: xtc trr trj gro g96 pdb tng
Other options:
-nice <int> (19)
Set the nicelevel
-xvg <enum> (xmgrace)
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)
SEE ALSOgromacs(7)
More information about GROMACS is available at <http://www.gro‐
macs.org/>.
VERSION 5.0.6gmx-nmens(1)
