[gmx-users] Energy conservation issue

Erik Lindahl lindahl at sbc.su.se
Fri Oct 28 14:46:27 CEST 2005


> With a plain cut-off one of the biggest sources of error is the
> charge group based neighborlist.
> When I change the water topology from one charge group to
> three (one for each atom) or when I used a shift function for the LJ
> I get 0 drift in double precision (300 ps) and about -85 kJ/mol/ns
> for single precision.
> One can not expect that single precision does as good as double
> precision. But the -85 kJ/mol/ns is already very good and comparable
> to other errors introduced by the simulation setup, such a charge  
> group
> based neighborlists and PME approximations.

The main problem in single precision are the constraints - in testing  
we've actually achieved perfect conservation even with constraints,  
as long as the integration/constraint part is perfomed in double  
(requires hacking).

You can also play with ewald_rtol to improve energy conservation with  
PME. The current PME interacition form is optimized to be as close as  
possible to the "true" infinite coulomb sum - you could envision  
adding a small switching term to improve the energy conservation and/ 
or zeroing the net force sum from the lattice part, but this again  
requires hacking.


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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