1 .TH g_nmens 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
3 g_nmens - generates an ensemble of structures from the normal modes
5 .B VERSION 4.5.4-dev-20110404-bc5695c
8 .BI "\-v" " eigenvec.trr "
9 .BI "\-e" " eigenval.xvg "
10 .BI "\-s" " topol.tpr "
11 .BI "\-n" " index.ndx "
12 .BI "\-o" " ensemble.xtc "
14 .BI "\-[no]version" ""
23 \&\fB g_nmens\fR generates an ensemble around an average structure
24 \&in a subspace that is defined by a set of normal modes (eigenvectors).
25 \&The eigenvectors are assumed to be mass\-weighted.
26 \&The position along each eigenvector is randomly taken from a Gaussian
27 \&distribution with variance kT/eigenvalue.
30 \&By default the starting eigenvector is set to 7, since the first six
31 \&normal modes are the translational and rotational degrees of freedom.
33 .BI "\-v" " eigenvec.trr"
35 Full precision trajectory: trr trj cpt
37 .BI "\-e" " eigenval.xvg"
41 .BI "\-s" " topol.tpr"
43 Structure+mass(db): tpr tpb tpa gro g96 pdb
45 .BI "\-n" " index.ndx"
49 .BI "\-o" " ensemble.xtc"
51 Trajectory: xtc trr trj gro g96 pdb
55 Print help info and quit
57 .BI "\-[no]version" "no "
58 Print version info and quit
60 .BI "\-nice" " int" " 19"
63 .BI "\-xvg" " enum" " xmgrace"
64 xvg plot formatting: \fB xmgrace\fR, \fB xmgr\fR or \fB none\fR
66 .BI "\-temp" " real" " 300 "
69 .BI "\-seed" " int" " \-1"
70 Random seed, \-1 generates a seed from time and pid
72 .BI "\-num" " int" " 100"
73 Number of structures to generate
75 .BI "\-first" " int" " 7"
76 First eigenvector to use (\-1 is select)
78 .BI "\-last" " int" " \-1"
79 Last eigenvector to use (\-1 is till the last)
84 More information about \fBGROMACS\fR is available at <\fIhttp://www.gromacs.org/\fR>.