[gmx-developers] Drift in Conserved-Energy with Nose-Hoover thermostat
b.reuter at uni-kassel.de
Tue Jul 21 14:43:28 CEST 2015
thank you very much for your very helpfull answer.
Obviously we agree on the dubious nature of the linear drift and that
its origin from reduced precision round-off errors is doubtful.
In my opinion the occurence of a linear energy drift of this size could
indicate a bug in the program.
So I startet a more rigorous investigation and would like to share some
Graph of Verlet buffer-size vs. energy-drift size for single and double
Graph of the linear total energy drift for a buffer-size of 0.02nm:
Exemplary mdp and log files for a buffer-size of 0.02nm:
The investigated protein-water system consists of 22765 atoms, the
AMBER99SB-ILDN force field with TIP3P water was used, all simulations
were in the NVE-ensemble, GROMACS 4.6.7 was used.
I will repeat the tests with GROMACS 5.0 and for different test systems
(i.e. the lysozyme system from the popular lysozyme tutorial of Justin
Am 20/07/15 um 00:50 schrieb Shirts, Michael R. (mrs5pt):
> > Do I have to switch to double precision if I care about energy
> conservation, integrator symplecticity, phase space volume
> conservation and ergodicity?
> This sounds a like a good idea. If you are doing tests where this
> matters, use double precision. Sounds like the safest.
> > Since bigger round-off errors by reduced precision shouldn't
> accumulate linearly but at worst with Sqrt(N): Shouldn't one be
> worried about the occurence of a linear systematic error by only
> changing the precision from double to single in a calculation?
> Reduced precision errors only would be linear if the errors are
> uncorrelated, but it's not clear to me why roundoff errors would be
> > But if you have a constant downward drift of energy you must
> consider that there is less phase space volume at lower energies - so
> there is no volume conservation in phase space.
> Correct, for NVE. For NVT, the conserved energy is a bookkeeping
> number, it has nothing to do with the current phase space of the
> system. The thermostat is pumping in more energy so that the kinetic
> energy remains consistent with the desired temperature. We then
> actually have a steady state system, rather than an equilibrium
> system. The question is, how different is this distribution from the
> true equilibrium distribution?
> This is generally testable. For thermodynamic calculations (which is
> what one presumably is intrested in with a thermostat, rather than the
> dynamics ), what really matters is 1) whether the correct distribution
> is obtained within noise and 2) whether the sampling is ergodic. 2)
> is very hard to answer, but 1) can be checked by
> With the theory described here:
> Gromacs in single precisions seems to behave fine statistically for
> systems of a few hundred atoms.
> I suspect that there are subtle phenomena where the lack of exact
> symplecticness matters. I also believe from my testing (no full paper
> on this) that there aren't very many that occur in highly chaotic
> systems with hundreds of particles at NIT.
> I bet there are cases with just a few particles where the problems
> could become very obvious, however.
> Michael Shirts
> Associate Professor
> Department of Chemical Engineering
> University of Virginia
> michael.shirts at virginia.edu <mailto:michael.shirts at virginia.edu>
> (434) 243-1821
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