[gmx-users] Re: Energy is not conserved

[K.A. Feenstra]

Vishal Vaidyanathan wrote:
> Hi,
>   We ran some simulations of a water box (the one provided with gromacs)
> in the NVE ensemble (no temperature or pressure coupling) and found the
> energy to fluctuate wildly.

It might be instructive to have a short list of energy-spoiling factors:
- cut-off effects (can be solved by using PME or worked around by shifted functions)
- time step (can be solved by decreasing timestep)
- precision; after other factors are fixed, you can see the effect of
   using single or double precision.
One of the more counter-intuitive factors is, that decreasing timestep below
a certain point (fractions of a fs), actually *decreases* energy conservation;
this is caused by an increased relative effect of the round-off errors.

In one of my papers, I've discussed several of the more detailed effects:
K. Anton Feenstra, Berk Hess and Herman J. C. Berendsen. Improving
       Efficiency of Large Time-scale Molecular Dynamics Simulations of
       Hydrogen-rich Systems. (1999) J. Comput. Chem. 20 (8), 786-798
http://www.chem.vu.nl/staf/feenstra/articles/jcc-20-8-789-798-(1999).pdf


-- 
Groetjes,

Anton
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|        | Anton Feenstra                                            |
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