[gmx-users] Normal Mode Analysis

[Sathish Kumar]

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
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> >
>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>



-- 
regards
M.SathishKumar