for a system that big it should not cost anything significantly extra
for such a small LES region.
carlos
Kenley Barrett wrote:
> Thanks for your reply. My system is about 200000 atoms total (counting
> hydrogens), although only about 40,000 of those are protein atoms, the
> rest is water. The LES region would be about 131 atoms. I'm not sure
> how many copies I should use--this is my first time using LES. I was
> thinking 5-10 copies.
>
> Please let me know if you need any more information to clarify my
> question. And thanks again for your reply.
>
> Kenley
>
> On 4/23/06, *Adrian Roitberg* <roitberg.qtp.ufl.edu
> <mailto:roitberg.qtp.ufl.edu>> wrote:
>
> Kenley Barrett wrote:
> > Dear AMBER community,
> >
> > I am writing a proposal for a project in which I intend to use
> Locally
> > Enhanced Sampling. I don't have time to run preliminary
> simulations before
> > the proposal is due, but I need to estimate computational cost
> for the
> > project. What's a good way to estimate the increase in
> computational cost
> > caused by using LES?
> >
> > Thank you in advance for any suggestions.
> >
> > Kenley
> >
> It of course depends on how big is the replicated "LES" region,
> how many
> copies you wish to use and how large is the unreplicated section.
> If you email details we can help you a bit.
>
> adrian
>
>
> --
> Dr. Adrian E. Roitberg
> Associate Professor
> Quantum Theory Project and Department of Chemistry
>
> University of Florida PHONE 352 392-6972
> P.O. Box 118435 FAX 352 392-8722
> Gainesville, FL 32611-8435 Email
> adrian.qtp.ufl.edu <mailto:adrian.qtp.ufl.edu>
> ============================================================================
>
> To announce that there must be no criticism of the president,
> or that we are to stand by the president right or wrong,
> is not only unpatriotic and servile, but is morally treasonable
> to the American public."
> -- Theodore Roosevelt
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Received on Wed Apr 26 2006 - 06:07:05 PDT
