[gmx-developers] energy conservation

David van der Spoel spoel at xray.bmc.uu.se
Fri Apr 7 17:54:38 CEST 2006


energy conservation seems to be a recurring topic. We are of course 
aware that different algorithms can degrade it. E.g. if you use 
constraints you will *never* get perfect energy conservation. The 
leap-frog integration algorithm is fine though. We have done microsecond 
simulations of water clusters with almost perfect energy conservation using:
- double precision
- no cut-offs (vacuum simulations)
- no thermostats
- settle for constraints
To the degree that energy conservation is not perfect (<1e-4) this is 
probably due to using a finite timestep. We have similar results for 
proteins with H-bonds constrained (using SHAKE) in water clusters, in 
vacuum, but much shorter simulations.

I'm all for energy conserving algorithms, but there are limitations in 
some algorithms that are very hard to make perfect. As soon as you start 
making compromises, like a shake tolerance of 1e-8 is "good enough", 
then the whole argument is moot as far as I'm concerned...
Michael, you mention "drifting off the energy surface". What does that 
mean? Are there two (or multiple) independent energy surfaces between 
which systems can not move if energy is conserved? Also, if people are 
convinced of the necessity of energy conservation, that's fine but not 
science. Is there any proof of these claims you mention? People tend to 
have lots of opinions on these things, but not many have the patience 
necessary for systematically testing and publishing them.

I agree that not many published simulations are reproducible, but that 
usually is because people are sloppy in the methods section or in the 
description of results. By the way, how many people do actually try?

It would be interesting to know who the other "fairly smart" people are, 
so that we can comfort them, but let's not put names on the mailing 
list, unless they want to step forward and disucss things here. If there 
are reproducible problems we will fix them (read: if it's not on 
bugzilla there is no bug).

Sorry if this sounds like a rant,  but I would like to make clear that 
we do take these things seriously, and we're open to criticism that's 
based on facts, but not criticism that's based on opinions.

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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