HI David,
Yes I am going to play with smaller systems ... Just did this test to
see if having all frames in the trajectory helps ... The system has
6353 atoms, its a protein-DNA complex and I am trying to estimate the
binding dG from MMPBSA ... I don't think its very gigantic, but maybe I
am wrong for these calculations ...
Vlad
On 10/31/2013 12:44 PM, David A Case wrote:
> On Thu, Oct 31, 2013, Vlad Cojocaru wrote:
>> Below is a output snapshot ... I am guessing I am still far from
>> convergence .
> It is indeed very hard to converge quasiharmonic calculations. I'd again
> suggest working with a smaller problem and making sure you understand how
> everything works. Look at all the frequencies. The fact that you still have
> NaN in the heat capacity field suggests some problems, and you total entropies
> are not reasonable.
>
>> warning: setting vibrational entropy to zero for mode 19056 with vtemp
>> = -8049467.209940
> This seems like more than a warning--something is quite wrong. Look at the
> frequency and other data for mode 19056 -- do you really have this many
> degrees of freedom? If so, you are trying to get results for a gigantic
> system that is larger than any I have ever had success with. Are there
> published calculations that do a similar analysis?
>
>> freq. E Cv S
>> cm**-1 kcal/mol cal/mol-kelvin cal/mol-kelvin
>> --------------------------------------------------------------------------------
>> Total 57372.075 -nan 23444.731
>> translational 0.888 2.979 58.245
>> rotational 0.888 2.979 62.369
>> vibrational 57370.299 -nan 23324.117
> Ditto for the numbers above.
>
> ...dac
>
>
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--
Dr. Vlad Cojocaru
Max Planck Institute for Molecular Biomedicine
Department of Cell and Developmental Biology
Röntgenstrasse 20, 48149 Münster, Germany
Tel: +49-251-70365-324; Fax: +49-251-70365-399
Email: vlad.cojocaru[at]mpi-muenster.mpg.de
http://www.mpi-muenster.mpg.de/research/teams/groups/rgcojocaru
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Received on Thu Oct 31 2013 - 06:30:03 PDT
