[gmx-users] Fwd: Normal Mode Analysis
sathishk238 at gmail.com
Mon Dec 9 05:21:57 CET 2013
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
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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