I can't answer your question for sure, but I do know that the instantaneous
temperature depends on the number of degrees of freedom of the system (so
it depends on connectivity, constraints, etc.).
I don't know of any instantaneous temperature formalism other than average
kinetic energy, so I would boldly assume that that is the one at play.
Although that's not particularly helpful because of at least two other
things I don't know:
1.) which velocities are used? since AMBER uses leap frog verlet it might
depend on the thermostat?
2) the averaging could probably be done in a few, possibly nonequivalent,
ways. I don't think averaging over atomic centers and molecular centers is
the same (geometric vs center of mass velociites?)
The fastest way to find out might be to check the source code.
Brian
On Thu, Jan 5, 2012 at 12:01 PM, Jan-Philip Gehrcke <jgehrcke.googlemail.com
> wrote:
> Huhu,
>
> sander/pmemd calculated the temperature of the simulated system for a
> given point in time and prints it to e.g. the mdout file.
>
> I just want to make sure.. is this value calculated from the average
> kinetic energy of all atoms in the system and the Boltzmann constant or
> is some other formalism applied?
>
> Thanks,
>
> Jan-Philip
>
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>
--
================================ Current Address =======================
Brian Radak : BioMaPS
Institute for Quantitative Biology
PhD candidate - York Research Group : Rutgers, The State
University of New Jersey
University of Minnesota - Twin Cities : Center for Integrative
Proteomics Room 308
Graduate Program in Chemical Physics : 174 Frelinghuysen Road,
Department of Chemistry : Piscataway, NJ
08854-8066
radak004.umn.edu :
radakb.biomaps.rutgers.edu
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Received on Thu Jan 05 2012 - 13:00:03 PST
