<html><head></head><body><div style="font-family: Verdana;font-size: 12.0px;"><div>
<div>So, my answere now is you need the correct vector (s). Made me check myself real quick though...but the tutorial and manual explain it well.</div>
<div> </div>
<div>Sorry again,</div>
<div> </div>
<div>Stephan</div>
<div>
<div name="quote" style="margin:10px 5px 5px 10px; padding: 10px 0 10px 10px; border-left:2px solid #C3D9E5; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;">
<div style="margin:0 0 10px 0;"><b>Gesendet:</b> Dienstag, 26. November 2013 um 07:43 Uhr<br/>
<b>Von:</b> "Tsjerk Wassenaar" <tsjerkw@gmail.com><br/>
<b>An:</b> "Discussion list for GROMACS users" <gmx-users@gromacs.org><br/>
<b>Betreff:</b> Re: [gmx-users] Normal Mode Analysis</div>
<div name="quoted-content">Hi Stephen,<br/>
<br/>
You're confusing NMA with PCA.<br/>
<br/>
Cheers,<br/>
<br/>
Tsjerk<br/>
<br/>
<br/>
On Tue, Nov 26, 2013 at 6:30 AM, lloyd riggs <lloyd.riggs@gmx.ch> wrote:<br/>
<br/>
> I don't know your energy break down, if you look at frames with g_anaeig<br/>
> using -first and -last to set your vector number(s), and then frames set to<br/>
> your time units desired, it will give you something you can look at with<br/>
> vmd or pymol. I have noticed though after the frst 4 or so vectors, it<br/>
> becomes dificult to see movement, as the enrgy break down for even larger<br/>
> proteins starts to become close to single amino acid or very small single<br/>
> atom contributions to the entire energy landscape. Thus hard to spot<br/>
> visually, as the enrgies might be only one or two high energy hydrogen<br/>
> bonds, etc...<br/>
><br/>
> Stephan Watkins<br/>
> *Gesendet:* Montag, 25. November 2013 um 17:05 Uhr<br/>
> *Von:* "Sathish Kumar" <sathishk238@gmail.com><br/>
> *An:* "Discussion list for GROMACS users" <gmx-users@gromacs.org><br/>
> *Betreff:* [gmx-users] Normal Mode Analysis<br/>
> 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/>
> --<br/>
> Gromacs Users mailing list<br/>
><br/>
> * Please search the archive at<br/>
> <a href="http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List</a> before<br/>
> posting!<br/>
><br/>
> * Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br/>
><br/>
> * For (un)subscribe requests visit<br/>
> <a href="https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users" target="_blank">https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users</a> or<br/>
> send a mail to gmx-users-request@gromacs.org.<br/>
> ------------------------------<br/>
> Diese E-Mail wurde aus dem Sicherheitsverbund E-Mail made in Germany<br/>
> versendet: <a href="http://www.gmx.net/e-mail-made-in-germany" target="_blank">http://www.gmx.net/e-mail-made-in-germany</a><<a href="http://www.gmx.net/e-mail-made-in-germany?mc=footer@textlink@emig.emig" target="_blank">http://www.gmx.net/e-mail-made-in-germany?mc=footer@textlink@emig.emig</a>><br/>
><br/>
> --<br/>
> Gromacs Users mailing list<br/>
><br/>
> * Please search the archive at<br/>
> <a href="http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List</a> before<br/>
> posting!<br/>
><br/>
> * Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br/>
><br/>
> * For (un)subscribe requests visit<br/>
> <a href="https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users" target="_blank">https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users</a> or<br/>
> send a mail to gmx-users-request@gromacs.org.<br/>
><br/>
><br/>
<br/>
<br/>
--<br/>
Tsjerk A. Wassenaar, Ph.D.<br/>
--<br/>
Gromacs Users mailing list<br/>
<br/>
* Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List</a> before posting!<br/>
<br/>
* Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br/>
<br/>
* For (un)subscribe requests visit<br/>
<a href="https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users" target="_blank">https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users</a> or send a mail to gmx-users-request@gromacs.org.</div>
</div>
</div>
</div></div><hr>
Diese E-Mail wurde aus dem Sicherheitsverbund E-Mail made in
Germany versendet: <a href="http://www.gmx.net/e-mail-made-in-germany?mc=footer@textlink@emig.emig">http://www.gmx.net/e-mail-made-in-germany</a></body></html>