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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>
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 - 12:30:03 PDT
