[gmx-users] Conserved energy ("Conserved En.") in NVT simulation

Mark Abraham mark.j.abraham at gmail.com
Wed Jul 31 20:54:48 CEST 2013

On Wed, Jul 31, 2013 at 7:47 PM, Janne Hirvi <janne.hirvi at uef.fi> wrote:
> Dear gmx-users,
> I have run some tests (especially) for pure water, being able to achieve pretty much perfect energy conservation in
> NVE ensemble (with PME-switch and shifted VDW potential).


> Then, just for the test, I continued to NVT ensemble by using previous .tpr and .cpt files, but the result was a quite
> surprise, because there seems to be constant drift in "Conserved En.".
> The drift (100kJ/mol = 0.3%) is not especially large, but it exists with v-rescale temperature coupling. On the other
> hand, there is no drift at all, if I change to nose-hoover temperature coupling.
> The behavior is similar also my other systems (liquid mixtures), even though then neither of temperature coupling
> methods will give exactly perfect conservation, but nose-hoover gives much better one (500 kJ/mol = 3% vs. 60
> kJ/mol = 0.4%).
> Actually, I was expecting to see no drift at all, after all systems behaved fine in NVE ensemble with same parameters
> with an exception of added temperature coupling (especially when I used double precision for test purpose).
> So, the main question is, if it is just normal that even such parameters, which give perfect energy conservation in NVE
> ensemble may introduce drift in "Conserved En.", when NVT ensemble is used? Or is it just purely (only reason for drift)
> indication that some temperature coupling methods"work better" than others in this sense?

In the case of v-rescale, the description of "Conserved En." is an
overbid. If you see the Bussi 2007 paper, there is a conserved
quantity H-tilde, but computing it requires knowledge of the whole of
history. IIRC their H is what mdrun reports as "Conserved En.". I
don't know whether it can be shown that a linear trend in H is
equivalent to conservation in H-tilde, but that would be a useful


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