[gmx-users] LR coulomb interaction ?

Michal Kolinski mkolin at iimcb.gov.pl
Thu May 5 14:49:17 CEST 2005

Thank you for comment. 
Could you please explain why do I need more reruns.
I'm looking for interaction ligand-protein, not ligand-system.
 In may case:
1 = LR (lig-lig)    . terms for rest, and prot = 0 
2 = LR (prot-prot)  .. terms for rest, and lig = 0
3 = LR (lig-lig) + LR (lig-prot) + LR (prot-prot)

LR (lig-prot) = 3 -1 -2 

For every rerun, for groups mentioned above, rest 
( which means other groups than protein and ligand) , I assigned charges = zero.
The LR coulomb energy calculated using g_energy gives total LR coulomb energy for all the groups with non zero charges, 
so it doesn't involve any terms that came from the rest groups with charges equal zero.  
Could you please  explain why do I need more reruns, I guess I missed something.
(I also include LR correction (-rerun -debug) in my calculations, my estimated LR Coulomb
interaction energy for ligand-protein seems wrong. Elr = 13.6)
Thank you in advance.  
Michal K.
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