1 .TH g_nmeig 1 "Thu 26 Aug 2010" "" "GROMACS suite, VERSION 4.5"
3 g_nmeig - diagonalizes the Hessian
8 .BI "\-f" " hessian.mtx "
9 .BI "\-s" " topol.tpr "
10 .BI "\-of" " eigenfreq.xvg "
11 .BI "\-ol" " eigenval.xvg "
12 .BI "\-v" " eigenvec.trr "
14 .BI "\-[no]version" ""
21 \&g_nmeig calculates the eigenvectors/values of a (Hessian) matrix,
22 \&which can be calculated with \fB mdrun\fR.
23 \&The eigenvectors are written to a trajectory file (\fB \-v\fR).
24 \&The structure is written first with t=0. The eigenvectors
25 \&are written as frames with the eigenvector number as timestamp.
26 \&The eigenvectors can be analyzed with \fB g_anaeig\fR.
27 \&An ensemble of structures can be generated from the eigenvectors with
28 \&\fB g_nmens\fR. When mass weighting is used, the generated eigenvectors
29 \&will be scaled back to plain cartesian coordinates before generating the
30 \&output \- in this case they will no longer be exactly orthogonal in the
31 \&standard cartesian norm (But in the mass weighted norm they would be).
33 .BI "\-f" " hessian.mtx"
37 .BI "\-s" " topol.tpr"
39 Structure+mass(db): tpr tpb tpa gro g96 pdb
41 .BI "\-of" " eigenfreq.xvg"
45 .BI "\-ol" " eigenval.xvg"
49 .BI "\-v" " eigenvec.trr"
51 Full precision trajectory: trr trj cpt
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
67 Divide elements of Hessian by product of sqrt(mass) of involved atoms prior to diagonalization. This should be used for 'Normal Modes' analysis
69 .BI "\-first" " int" " 1"
70 First eigenvector to write away
72 .BI "\-last" " int" " 50"
73 Last eigenvector to write away
78 More information about \fBGROMACS\fR is available at <\fIhttp://www.gromacs.org/\fR>.