[gmx-users] Fwd: Normal Mode Analysis

Sathish Kumar sathishk238 at gmail.com
Fri Dec 6 15:33:13 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

I was calculated the eigen vectors, eigen values and eigen frequences by
using the following command

g_nmeig_d -f nm.mtx -s nm1.tpr -of -ol -v -first 7 -last 10000

I generated ensemble of structures with the help of eigen vectors by using
the commands

g_nmens_d -v eigenvec.trr -e eigenval.xvg -s nm.tpr -n index.ndx -o
ensemble.xtc -num 5000

For the analysis of eigen vectors i used the following commands

g_anaeig_d -s nm1.tpr -f ensemble.xtc -v eigenvec.trr -eig eigenval.xvg
-extr ev1.pdb -first 7 -last 10 -nframes 30

by visuvalizing ev1.pdb, in PYMOL software it was not show any movement of

Is this correct process for NM analysis and how can i get the motion
corresponding to each eigen vector.

     Thank You.

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