[gmx-developers] DIfference in Coulomb terms 5.0/4.6

Berk Hess hess at kth.se
Sun Nov 16 16:24:10 CET 2014


The exclusion correction for both PME and RF is calculated in the non-bonded kernel with the Verlet scheme. As you mailed before, the energy matches exactly.



On Nov 16, 2014 2:53 PM, David van der Spoel <spoel at xray.bmc.uu.se> wrote:
> On 2014-11-15 19:34, Berk Hess wrote: 
> > Hi, 
> > 
> > Is this group vs Verlet cutoff scheme? With the Verlet Cutoff's scheme the subtraction of the reciprocal component for excluded pair has been moved from the reciprocal term to the SR term. 
> > That is not really debugging, since the division is not based on physics and thus there is no bug. 
> > Additionally the automated PME load balancing can change beta, thereby changing the distribution of the total Coulomb energy over the two terms. 
> > 
> Thanks. There is more though. I find that the exclusion/self corrections 
> are turned off when using Verlet scheme. 
> The routine ewald_LRcorrection is called (in both 4.6.x and 5.0.x) such 
> that the variable calc_excl_corr is set as ir->cutoff_scheme != 
> ecutsVERLET. This means in practice that with the Verlet scheme the self 
> and exclusion corrections are 0. 
> Is this intentional? The effect is a large energy difference between 
> systems in the two versions (we are trying to get the polarizable drude 
> water working). 
> -- 
> David van der Spoel, Ph.D., Professor of Biology 
> Dept. of Cell & Molec. Biol., Uppsala University. 
> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. 
> spoel at xray.bmc.uu.se    http://folding.bmc.uu.se 
> -- 
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