Dear Sir,
I have already simulated many small complexes using plain molecular
dynamics. But, as i know, Amber is restricted for systems < 100,000 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??
Regards
kshatresh
On Sun, Dec 5, 2010 at 8:31 PM, case <case.biomaps.rutgers.edu> wrote:
> On Sun, Dec 05, 2010, Kshatresh Dutta Dubey wrote:
> >
> > I am interested in metadynamic simulation of a huge protein containing
> more
> > than 200,000 atoms. Recently, i saw a reply where adaptively biased
> > molecular dynamics is stated for this purpose. I am presently using Amber
> > 10. Can i use this program for this system?
>
> Metadynamics is an advanced application, and one you should not try until
> you
> are sure you can run successful (and long) regular dynamics simulations on
> your system.
>
> If you are new to Amber (and/or simulations in general), gaining experience
> with smaller systems first is highly recommended.
>
> ...dac
>
>
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Received on Sun Dec 05 2010 - 21:00:04 PST
