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

6       g_nmeig - diagonalizes the Hessian
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8       VERSION 4.5
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SYNOPSIS

11       g_nmeig  -f hessian.mtx -s topol.tpr -of eigenfreq.xvg -ol eigenval.xvg
12       -v eigenvec.trr -[no]h -[no]version -nice int -xvg enum  -[no]m  -first
13       int -last int
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DESCRIPTION

16       g_nmeig calculates the eigenvectors/values of a (Hessian) matrix, which
17       can be calculated with  mdrun.  The eigenvectors are written to a  tra‐
18       jectory  file  (  -v).   The  structure  is written first with t=0. The
19       eigenvectors are written as frames with the eigenvector number as time‐
20       stamp.   The  eigenvectors can be analyzed with  g_anaeig.  An ensemble
21       of structures can be generated from the  eigenvectors  with    g_nmens.
22       When  mass weighting is used, the generated eigenvectors will be scaled
23       back to plain cartesian coordinates before generating the output  -  in
24       this  case  they  will  no longer be exactly orthogonal in the standard
25       cartesian norm (But in the mass weighted norm they would be).
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FILES

28       -f hessian.mtx Input
29        Hessian matrix
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31       -s topol.tpr Input
32        Structure+mass(db): tpr tpb tpa gro g96 pdb
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34       -of eigenfreq.xvg Output
35        xvgr/xmgr file
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37       -ol eigenval.xvg Output
38        xvgr/xmgr file
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40       -v eigenvec.trr Output
41        Full precision trajectory: trr trj cpt
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OTHER OPTIONS

45       -[no]hno
46        Print help info and quit
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48       -[no]versionno
49        Print version info and quit
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51       -nice int 19
52        Set the nicelevel
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54       -xvg enum xmgrace
55        xvg plot formatting:  xmgrace,  xmgr or  none
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57       -[no]myes
58        Divide elements of Hessian by product of sqrt(mass) of involved  atoms
59       prior to diagonalization. This should be used for 'Normal Modes' analy‐
60       sis
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62       -first int 1
63        First eigenvector to write away
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65       -last int 50
66        Last eigenvector to write away
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SEE ALSO

70       gromacs(7)
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72       More  information  about  GROMACS  is  available  at   <http://www.gro‐
73       macs.org/>.
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77                                Thu 26 Aug 2010                     g_nmeig(1)
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