[gmx-developers] bug in 407 with charge groups

David van der Spoel spoel at xray.bmc.uu.se
Tue Nov 2 13:31:57 CET 2010

A local user here brought to my attention that in 4.0.7 there is a 
serious bug due to charge groups. If you have a small molecule with all 
atoms in one charge group and infinite cutoffs in vacuo the energy is 
wrong. If you put each atom in it's own charge group the result is 
correct (as compared to Macromodel). The reason appears to be that the 
neighborlist is incorrect:

1 cg/molecule
<  Coulomb + LJ                       0.000569           0.022    29.0
1 cg/atom
 >  Coulomb + LJ                       0.000620           0.024    24.9

in other words, 51 interactions are left out. In 4.5.x this bug is no 
longer there, so it would be good if the fix that went into 4.0.x as 
well. I can't seem to find any notion of this being fixed in the git 
logs of ns.c though.
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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