[gmx-users] Energy conservation issue

Erik Lindahl lindahl at sbc.su.se
Fri Oct 28 23:40:57 CEST 2005

> Why not remove this big source of error (BSOE), especially when
> Ewald/PME/PPPM is used. (Or maybe add a mdp option for the user to
> choose, but I doubt anyone would like to choose the BSOE :-) I imagine
> this change just requires a few line of code.

Well, it's trivial to change yourself in the topology or rtp file :-)

There are a couple of reasons why we don't do it by default:

1. Several force fields are designed with charge groups, and have  
been used that way for years. Regardless of whether we like that or  
we want results to be reproducible.

2. Neighborsearching can be pretty expensive with our fast  
innerloops, sometimes 30-40% of the total runtime. Group-based NS is  

> I love to hear this. Many people still consider achieving (nearly)
> perfect energy conservation (for an isolated system) in single  
> precision
> will be a big advantage. And I believe performing the integration  
> and/or
> constraints in double precision will have negligible overhead, so I
> would love to see this "hacking" can be made default inside Gromacs.

The overhead would probably be insignificant on a standard x86 CPU,  
but Gromacs is also used on hardware where double precision has to be  
simulated and is insanely expensive (embedded CPUs, graphics cards,  

If at all possible I'd rather like to understand exactly _where_ we  
loose the accuracy and perform only that step on double, instead of  
converting entire arrays to double (Using bonds instead of  
constraints will conserve energy).

We do realize that some users really want energy conservation and  
will try to make it easier to achieve "by default", but our rationale  
has been that per se it doesn't tell you anything about accuracy  
(imagine a switched cutoff at 1A, or changing sign of the coulomb  
term) - and remember that we are usually distorting the interaction  
form to achieve the conservative potential with cutoffs!



Erik Lindahl  <lindahl at sbc.su.se>
Assistant Professor, Stockholm Bioinformatics Center
Stockholm University, SE 106 91 Stockholm
Phone: +46 8 5537 8564     Fax: +46 8 5537 8214

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