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.TH "GMX-NMENS" "1" "Feb 15, 2019" "2019.1" "GROMACS"
.SH NAME
gmx-nmens \- Generate an ensemble of structures from the normal modes
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.SH SYNOPSIS
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gmx nmens [\fB\-v\fP \fI[<.trr/.cpt/...>]\fP] [\fB\-e\fP \fI[<.xvg>]\fP] [\fB\-s\fP \fI[<.tpr/.gro/...>]\fP]
          [\fB\-n\fP \fI[<.ndx>]\fP] [\fB\-o\fP \fI[<.xtc/.trr/...>]\fP] [\fB\-xvg\fP \fI<enum>\fP]
          [\fB\-temp\fP \fI<real>\fP] [\fB\-seed\fP \fI<int>\fP] [\fB\-num\fP \fI<int>\fP] [\fB\-first\fP \fI<int>\fP]
          [\fB\-last\fP \fI<int>\fP]
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.fi
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.SH DESCRIPTION
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\fBgmx nmens\fP 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.
.sp
By default the starting eigenvector is set to 7, since the first six
normal modes are the translational and rotational degrees of freedom.
.SH OPTIONS
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Options to specify input files:
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.B \fB\-v\fP [<.trr/.cpt/…>] (eigenvec.trr)
Full precision trajectory: trr cpt tng
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.B \fB\-e\fP [<.xvg>] (eigenval.xvg)
xvgr/xmgr file
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.B \fB\-s\fP [<.tpr/.gro/…>] (topol.tpr)
Structure+mass(db): tpr gro g96 pdb brk ent
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.B \fB\-n\fP [<.ndx>] (index.ndx) (Optional)
Index file
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Options to specify output files:
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.B \fB\-o\fP [<.xtc/.trr/…>] (ensemble.xtc)
Trajectory: xtc trr gro g96 pdb tng
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Other options:
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.B \fB\-xvg\fP <enum> (xmgrace)
xvg plot formatting: xmgrace, xmgr, none
.TP
.B \fB\-temp\fP <real> (300)
Temperature in Kelvin
.TP
.B \fB\-seed\fP <int> (0)
Random seed (0 means generate)
.TP
.B \fB\-num\fP <int> (100)
Number of structures to generate
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.B \fB\-first\fP <int> (7)
First eigenvector to use (\-1 is select)
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.B \fB\-last\fP <int> (\-1)
Last eigenvector to use (\-1 is till the last)
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.SH SEE ALSO
.sp
\fBgmx(1)\fP
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More information about GROMACS is available at <\fI\%http://www.gromacs.org/\fP>.
.SH COPYRIGHT
2019, GROMACS development team
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