1g_nmens(1)                GROMACS suite, VERSION 4.5                g_nmens(1)
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NAME

6       g_nmens - generates an ensemble of structures from the normal modes
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8       VERSION 4.5
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SYNOPSIS

11       g_nmens  -v  eigenvec.trr  -e eigenval.xvg -s topol.tpr -n index.ndx -o
12       ensemble.xtc -[no]h -[no]version -nice int -xvg enum -temp  real  -seed
13       int -num int -first int -last int
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DESCRIPTION

16         g_nmens  generates  an ensemble around an average structure in a sub‐
17       space which is defined by a set of normal  modes  (eigenvectors).   The
18       eigenvectors  are assumed to be mass-weighted.  The position along each
19       eigenvector is randomly taken from a Gaussian distribution  with  vari‐
20       ance kT/eigenvalue.
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23       By  default  the  starting eigenvector is set to 7, since the first six
24       normal modes are the translational and rotational degrees of freedom.
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FILES

27       -v eigenvec.trr Input
28        Full precision trajectory: trr trj cpt
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30       -e eigenval.xvg Input
31        xvgr/xmgr file
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33       -s topol.tpr Input
34        Structure+mass(db): tpr tpb tpa gro g96 pdb
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36       -n index.ndx Input, Opt.
37        Index file
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39       -o ensemble.xtc Output
40        Trajectory: xtc trr trj gro g96 pdb
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OTHER OPTIONS

44       -[no]hno
45        Print help info and quit
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47       -[no]versionno
48        Print version info and quit
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50       -nice int 19
51        Set the nicelevel
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53       -xvg enum xmgrace
54        xvg plot formatting:  xmgrace,  xmgr or  none
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56       -temp real 300
57        Temperature in Kelvin
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59       -seed int -1
60        Random seed, -1 generates a seed from time and pid
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62       -num int 100
63        Number of structures to generate
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65       -first int 7
66        First eigenvector to use (-1 is select)
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68       -last int -1
69        Last eigenvector to use (-1 is till the last)
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SEE ALSO

73       gromacs(7)
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75       More  information  about  GROMACS  is  available  at   <http://www.gro‐
76       macs.org/>.
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80                                Thu 26 Aug 2010                     g_nmens(1)
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