[gmx-users] Fwd: Normal Mode Analysis

Joaquim Rui de Castro Rodrigues joaquim.rodrigues at ipleiria.pt
Tue Dec 10 13:08:56 CET 2013

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

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?

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