[gmx-users] LR coulomb interaction

[Michal Kolinski]

I tried to evaluate LR Coulomb interaction energy for ligand and protein.  My system contains
membrane, ligand, TM protein and ions.  I did three reruns of my trajectory:
1) leaving charges on ligand, zeroing rest 
2) leaving charges on protein, zeroing rest 
3) leaving charges on protein and ligand, zeroing rest.
Then I calculated LR Coulomb interaction energy for prot-lig (Elr_c(ligand-protein)):


Elr_c(protein-ligand) = Elr_c(ligand-ligand) + Elr_c(ligand-protein) +
                                      Elr_c(protein-protein) 
      in my case:

3 = 1 +  Elr_c(ligand-protein) + 2

 I also included long range corrections for each of the reruns that I found using -rerun -debug option.  
Is this a right way to estimate LR coulomb interaction energy between two molecules, my estimated energy seems wrong  13.567.
 Please give me some comment on this.
Thank you in advance. 

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20050504/98ce9709/attachment.html>