[gmx-users] Normal Mode Analysis

[Sathish Kumar]

Thank you for your suggestions.


On Wed, Nov 27, 2013 at 5:30 AM, lloyd riggs <lloyd.riggs at gmx.ch> wrote:

> Sorry,
>
> Your correct. Thanks for correcting me.  I dont want to send people off on
> tangents, and thus appologise.
>
> Stephan
>
> *Gesendet:* Dienstag, 26. November 2013 um 07:43 Uhr
> *Von:* "Tsjerk Wassenaar" <tsjerkw at gmail.com>
> *An:* "Discussion list for GROMACS users" <gmx-users at gromacs.org>
> *Betreff:* Re: [gmx-users] Normal Mode Analysis
> Hi Stephen,
>
> You're confusing NMA with PCA.
>
> Cheers,
>
> Tsjerk
>
>
> On Tue, Nov 26, 2013 at 6:30 AM, lloyd riggs <lloyd.riggs at gmx.ch> wrote:
>
> > I don't know your energy break down, if you look at frames with g_anaeig
> > using -first and -last to set your vector number(s), and then frames set
> to
> > your time units desired, it will give you something you can look at with
> > vmd or pymol. I have noticed though after the frst 4 or so vectors, it
> > becomes dificult to see movement, as the enrgy break down for even larger
> > proteins starts to become close to single amino acid or very small single
> > atom contributions to the entire energy landscape. Thus hard to spot
> > visually, as the enrgies might be only one or two high energy hydrogen
> > bonds, etc...
> >
> > Stephan Watkins
> > *Gesendet:* Montag, 25. November 2013 um 17:05 Uhr
> > *Von:* "Sathish Kumar" <sathishk238 at gmail.com>
> > *An:* "Discussion list for GROMACS users" <gmx-users at gromacs.org>
> > *Betreff:* [gmx-users] Normal Mode Analysis
> > 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