On Fri, Jan 06, 2012, Jan-Philip Gehrcke wrote:
> I've been going through pmemd source a bit. Temperature is definitely
> calculated from kinetic energy, number of degrees of freedom and the
> Boltzmann constant, but I am still not sure about the details.
> Especially, I am a bit confused by an apparent distinction between
> solvent and solute atoms during temperature calculation.
I think that pmemd actually makes no distinction between "solute" and
"solvent" atoms; code describing such distinction is probably left over from
much earlier days, when sander (which pmemd tries to mimic) made that
distinction. (Sander doesn't make any use of such a division either).
...good luck...dac
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Received on Sat Jan 07 2012 - 10:00:03 PST
