AMBER Archive (2006)

Subject: Re: AMBER: increase in computational time with LES

From: Kenley Barrett (kenley.barrett_at_gmail.com)
Date: Sun Apr 23 2006 - 17:46:56 CDT

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_at_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_at_qtp.ufl.edu
>
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