[gmx-users] LR coulomb interaction ?

Michal Kolinski mkolin at iimcb.gov.pl
Thu May 5 14:53:38 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 run, 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.
Thank you in advance.  

On Wed, 2005-05-04 at 19:37 +0200, 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) 

principle is right, but where is the membrane and solvent? You probably
need more reruns..'

>       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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