On Mon, Dec 06, 2010, Kshatresh Dutta Dubey wrote:
>
> I have already simulated many small complexes using plain molecular
> dynamics. But, as i know, Amber is restricted for systems < 100,000 atoms.
This is not correct. We test Amber on systems several times this large, and
have some test cases with more than a million atoms.
> When i am using solvation box for a protein in trimeric form, the number of
> atoms exceeds 200,000 which is causing some errors in coordinate
> preparation. Here, i am interested in simulation in trimeric form. So, is
> there any idea to run simulation for this system??
We would need to know more about the "errors in coordinate preparation."
...dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Dec 06 2010 - 05:00:03 PST
