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
> > _______________________________________________
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> > 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
