[gmx-users] Re: Minimization before NMA

[nahren manuel]

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 <vvchaban at gmail.com> wrote:

From: Vitaly Chaban <vvchaban at gmail.com>
Subject: [gmx-users] Re: Minimization before NMA
To: gmx-users at gromacs.org
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
>
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