[gmx-users] LR coulomb interaction

Steven Spronk spronk at its.caltech.edu
Thu May 5 19:31:50 CEST 2005

Hi Michal,

It sounds like we are doing similar things.

Can you explain to me how you were able to use mdrun -rerun -debug to get
the correction terms?  I tried running this yesterday, and it generated
some files (ctab.xvg, dtab.xvg, rtab.xvg, mdrun.log), but I have no idea
where to look for the correction.


On Wed, 4 May 2005, Michal Kolinski wrote:

> 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.

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