Re: [AMBER] softcore potential and temperature

From: <anyiphysics.gmail.com>
Date: Tue, 26 Apr 2011 21:39:02 +0000

Thanks Thomas,

I think my SC region behaves normally.

Yi


On Apr 26, 2011 2:25pm, steinbrt.rci.rutgers.edu wrote:
> Hi,



> that depends. If your softcore region is small, you will see larger

> fluctuations than for a full MM-system, up to hundreds of K for a single

> SC atom. This is normal I believe. You should get the correct average over

> a longer simulation though. Still, look at your trajectories to check if

> the SC region behaves normally to make sure.



> Thomas



> On Tue, April 26, 2011 2:19 pm, anyiphysics.gmail.com wrote:

> > Dear AMBER users,

> >

> > I'm using softcore potential to calculate binding energy between a DNA
> and

> > its antibody. I realized that the temperatures in the softcore section

> > fluctuate a lot even though I set temp0 = 300. It is normal or should I

> > correct something in my input file?

> > Thank you in advance.

> >

> > Yi An

> > graduate student

> > Texas A&M university

> > _______________________________________________

> > AMBER mailing list

> > AMBER.ambermd.org

> > http://lists.ambermd.org/mailman/listinfo/amber

> >





> Dr. Thomas Steinbrecher

> formerly at the

> BioMaps Institute

> Rutgers University

> 610 Taylor Rd.

> Piscataway, NJ 08854



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Received on Tue Apr 26 2011 - 15:00:02 PDT
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