[AMBER] Virial and Kinetic energy

From: Iain Bethune <i.bethune.epcc.ed.ac.uk>
Date: Tue, 23 May 2017 11:47:10 +0100

Hi Amber folks,

I am interested in measuring the temperature of systems using alternatives to the standard temperature derived from the instantaneous kinetic energy via the equipartition theorem. In particular, the virial theorem says that:

<KE> = -1/2 * sum_i < F_k . r_k>

Eventually (subject to fluctuations), I expect the KE computed via the virial and the instantaneous KE to converge to the same value (the ensemble average), or equivalently, the virial (sum of F.r over all particles) should be equal to -2 * the computed KE in the long timescale limit.

However, I have not found this to be the case, for example using the explicit water DNA 10-mer system from http://ambermd.org/tutorials/basic/tutorial1/section5.htm the averages are:

EKtot = 5956.8385
VIRIAL = 2940.6816

That is, the virial is somewhat less than half the KE, and is positive!

So my questions then are:

* How is the printed VIRIAL defined in Amber? I didn’t find anything in the user manual, unfortunately?
* Is there any way to directly print the sum of F.r for use in the above relation?


- Iain

Iain Bethune
Project Manager, EPCC
Email: i.bethune.epcc.ed.ac.uk
Twitter: .IainBethune @PrimeGrid @CP2Kproject
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Received on Tue May 23 2017 - 04:00:03 PDT
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