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<div>I don't know your energy break down, if you look at frames with g_anaeig using -first and -last to set your vector number(s), and then frames set to your time units desired, it will give you something you can look at with vmd or pymol. I have noticed though after the frst 4 or so vectors, it becomes dificult to see movement, as the enrgy break down for even larger proteins starts to become close to single amino acid or very small single atom contributions to the entire energy landscape. Thus hard to spot visually, as the enrgies might be only one or two high energy hydrogen bonds, etc...</div>
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<div>Stephan Watkins</div>
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<div style="margin:0 0 10px 0;"><b>Gesendet:</b> Montag, 25. November 2013 um 17:05 Uhr<br/>
<b>Von:</b> "Sathish Kumar" <sathishk238@gmail.com><br/>
<b>An:</b> "Discussion list for GROMACS users" <gmx-users@gromacs.org><br/>
<b>Betreff:</b> [gmx-users] Normal Mode Analysis</div>
<div name="quoted-content">Dear users,<br/>
<br/>
I am trying to do NMA<br/>
<br/>
First i did energy minimization using .mdp file with conjugate gradient<br/>
method,<br/>
<br/>
Next i calculated hessian matrix by using integrator = nm<br/>
<br/>
Then i calculated the eigen vectors from 7 to 100 using g_nmeig<br/>
<br/>
to analyze eigen vectors i use the commands<br/>
<br/>
g_anaeig_d -s nm.tpr -f em-c.gro -v eigenvec.trr -eig eigenval.xvg -proj<br/>
proj-ev1.xvg -extr<br/>
<br/>
ev1.pdb -rmsf rmsf-ev1.xvg -first 7 -last 7 -nframes 30<br/>
<br/>
<br/>
by visuvalizing ev1.pdb, i did not found any motion in the protein.<br/>
<br/>
<br/>
what is the mistake i have done?<br/>
<br/>
Is it correct procedure for doing NM analysis?<br/>
<br/>
How to analyze the eigen values obtained from hessian matrix?<br/>
<br/>
<br/>
regards<br/>
M.SathishKumar<br/>
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