[gmx-users] Fwd: Normal Mode Analysis

Sathish Kumar sathishk238 at gmail.com
Mon Dec 9 05:21:57 CET 2013

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?


More information about the gromacs.org_gmx-users mailing list