[gmx-users] LR coulomb interaction
mkolin at iimcb.gov.pl
Wed May 4 19:37:51 CEST 2005
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) +
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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