[gmx-users] Fwd: Normal Mode Analysis

Sathish Kumar sathishk238 at gmail.com
Tue Dec 10 14:33:00 CET 2013


Thank You very much for your reply, I will try by increasing the
temperature, up to at what temperature i can increase in pymol.




On Tue, Dec 10, 2013 at 5:37 PM, Joaquim Rui de Castro Rodrigues <
joaquim.rodrigues at ipleiria.pt> wrote:

> Dear Sathish,
>
> You are writing vectors 7-100 to eigenvec.trr using g_nmeig, and then ask
> g_anaeig_d to analyze the 7th vector of eigenvec.trr.
>
> Try running g_nmeig_d with default parameters:
> g_nmeig_d -f hessian.mtx -s nm.tpr
>
> and then generate an oscillating trajectory with
> g_nmtraj_d -s nm.tpr -v eigenvec.trr -eignr 7 -temp 10000
> for the 1st non-trivial mode, that can be read with pymol. You may want
> increase the temp value…
>
> Hope this helps,
> Rui Rodrigues
>
>
>
> ________________________________________
> De: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [
> gromacs.org_gmx-users-bounces at maillist.sys.kth.se] Em Nome De Sathish
> Kumar [sathishk238 at gmail.com]
> Enviado: segunda-feira, 9 de Dezembro de 2013 4:21
> Para: Discussion list for GROMACS users
> Assunto: [gmx-users] Fwd: 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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-- 
regards
M.SathishKumar


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