[gmx-users] Normal Mode Analysis

[Tsjerk Wassenaar]

Hi Sathish,

Have you tried reading the g_nmens manpage or the manual?

Cheers,

Tsjerk


On Mon, Nov 25, 2013 at 6:00 PM, Sathish Kumar <sathishk238 at gmail.com>wrote:

> Is that ensemble of structures are related to each eigen vector or total
> eigen vectors.
>
> If i want to see the motion of seventh eigen vector how can i get?
>
>
> On Mon, Nov 25, 2013 at 9:50 PM, Tsjerk Wassenaar <tsjerkw at gmail.com>
> wrote:
>
> > 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.
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>
>
> --
> regards
> M.SathishKumar
> --
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-- 
Tsjerk A. Wassenaar, Ph.D.