Re: [AMBER] Origin of calculated system temperature (in mdout file)

From: Brian Radak <radak004.umn.edu>
Date: Thu, 5 Jan 2012 15:50:10 -0500

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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>



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Received on Thu Jan 05 2012 - 13:00:03 PST
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