<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;">Dear Gromacs Users,<br>Thanks for your Reply.<br>Yes i did move forward to calculate the eigenvalues, as listed below.<br><br> 1 -1.0096<br> 2 -0.860704<br> 3 -0.621409<br> 4 -0.0477899<br> 5 -7.98079e-07<br> 6 -2.20151e-08<br> 7 2.76454e-06<br> 8 0.000416762<br> 9 0.000621199<br> 10 0.00206166<br>
11 0.0256563<br> 12 0.0287882<br> 13 0.0341334<br> 14 0.0540256<br> 15 0.103671<br> 16 0.107328<br> 17 0.117916<br> 18 0.152177<br> 19 0.177111<br> 20 0.204475<br> 21 0.211167<br> 22 0.249744<br> 23 0.259533<br>
24 0.26757<br> 25 0.293689<br>.<br>.<br>.<br>.<br><br>the first six eigenvalues should ideally be close to zero, but I such high negative value confuses me a little. So does this indicate my normal mode calculation is imperfect ?<br>Anyway these first 6 eigenvalues are infact not considered for calculation. The remaining eigenvalues are all non-negative. So I do not know if things are fine.<br><br>I am repeating the procedure with another starting structure from the MD run (the lowest energy snapshot).<br><br>Best,<br>nahren<br><br>--- On <b>Tue, 8/3/10, Vitaly Chaban <i><vvchaban@gmail.com></i></b> wrote:<br><blockquote style="border-left: 2px solid rgb(16, 16, 255); margin-left: 5px; padding-left: 5px;"><br>From: Vitaly Chaban <vvchaban@gmail.com><br>Subject: [gmx-users] Re: Minimization before NMA<br>To:
gmx-users@gromacs.org<br>Date: Tuesday, August 3, 2010, 1:53 AM<br><br><div class="plainMail">nahren:<br><br>Hmm... Why do you think Fmax=1.754e+00 is not enough for NMA?<br><br>Dr. Vitaly Chaban<br><br><br>> I am unable to minimize a complex protein (Trimer-Trimer complex) to even less than Fmax=1.754e+00.<br>><br>> I tried few tricks like performing MD for few steps etc, but it does not yield any results.<br>><br>> I am sure there must be a way out. Can you please advice.<br>><br>> Thanks for your attention.<br>><br>> nahren<br>><br>-- <br>gmx-users mailing list <a ymailto="mailto:gmx-users@gromacs.org" href="/mc/compose?to=gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>Please search the archive at <a href="http://www.gromacs.org/search"
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