Dear Gromacs Users, Thanks for your Reply. Yes i did move forward to calculate the eigenvalues, as listed below.
1 -1.0096 2 -0.860704 3 -0.621409 4 -0.0477899 5 -7.98079e-07 6 -2.20151e-08 7 2.76454e-06 8 0.000416762 9 0.000621199 10 0.00206166 11 0.0256563 12 0.0287882 13 0.0341334 14 0.0540256 15 0.103671 16 0.107328 17 0.117916 18 0.152177 19 0.177111 20 0.204475 21 0.211167 22 0.249744 23 0.259533 24 0.26757 25 0.293689 . . . . 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 ? 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. I am repeating the procedure with another starting structure from the MD run (the lowest energy snapshot). Best, nahren --- On Tue, 8/3/10, Vitaly Chaban <[email protected]> wrote: From: Vitaly Chaban <[email protected]> Subject: [gmx-users] Re: Minimization before NMA To: [email protected] Date: Tuesday, August 3, 2010, 1:53 AM nahren: Hmm... Why do you think Fmax=1.754e+00 is not enough for NMA? Dr. Vitaly Chaban > I am unable to minimize a complex protein (Trimer-Trimer complex) to even > less than Fmax=1.754e+00. > > I tried few tricks like performing MD for few steps etc, but it does not > yield any results. > > I am sure there must be a way out. Can you please advice. > > Thanks for your attention. > > nahren > -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
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