yes, this was a test with 8000 frames ..
The complex has 6353 atoms
The receptor has 3788 atoms
The ligand has 2565
My trajectory has in total 50000 frames .. I wanted to exclude the first
10000. So I'd be left with 40000 frames .. This would make about
6*Natoms of the largest system. However this is extremely expensive for
a 1 core job ...
Maybe I could give it a try with the parallel ptraj.
Best wishes
Vlad
On 10/29/2013 02:21 PM, David A Case wrote:
> On Tue, Oct 29, 2013, Vlad Cojocaru wrote:
>> Yes, I did superimpose (I provided a sample input for ptraj in my
>> previous email).
> How many snapshots do you have? You need to have (significantly) more
> snapshots than degrees of freedom in your system. I guessing(?) you may have
> exactly 8000 snapshots, but something like 6353 atoms. You need more than
> 3*natom snapshots at a minimum.
>
> ...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 Tue Oct 29 2013 - 07:00:02 PDT
