[gmx-users] Normal Mode Analysis

[Tsjerk Wassenaar]

>From g_nmeig -h:

An ensemble of structures can be generated from the eigenvectors with
g_nmens.

Cheers,

Tsjerk


On Mon, Nov 25, 2013 at 5:05 PM, Sathish Kumar <sathishk238 at gmail.com>wrote:

> Dear users,
>
>                    I am trying to do NMA
>
> First i did energy minimization using .mdp file with conjugate gradient
> method,
>
> Next i calculated hessian matrix by using integrator = nm
>
> Then i calculated the eigen vectors from 7 to 100 using g_nmeig
>
> to analyze eigen vectors i use the commands
>
> g_anaeig_d -s nm.tpr -f em-c.gro -v eigenvec.trr -eig eigenval.xvg -proj
> proj-ev1.xvg -extr
>
> ev1.pdb -rmsf rmsf-ev1.xvg -first 7 -last 7 -nframes 30
>
>
> by visuvalizing ev1.pdb, i did not found any motion in the protein.
>
>
> what is the mistake i have done?
>
> Is it correct procedure for doing NM analysis?
>
> How to analyze the eigen values obtained from hessian matrix?
>
>
> regards
> M.SathishKumar
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-- 
Tsjerk A. Wassenaar, Ph.D.