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Man Pages


Manual Reference Pages  -  GMX-NMENS (1)

NAME

gmx-nmens - Generate an ensemble of structures from the normal modes

CONTENTS

Synopsis
Description
Options
See Also

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 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 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 ALSO

gromacs(7)

More information about GROMACS is available at <http://www.gromacs.org/>.

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VERSION 5.0.6 GMX-NMENS (1)

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