[gmx-users] Normal Mode Analysis

[Tsjerk Wassenaar]

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.