[gmx-users] Long range interaction energy of charged particles with PME - GMX 3.3.1

Ran Friedman ran at hemi.tau.ac.il
Thu Jul 27 10:14:03 CEST 2006

Dear GMX users and developers,

I previously asked how to calculate the long range interactions between 
charged particles simulated with PME:

I repeat the question here. If I want to calculate the LR Coulomb 
interaction energy between say a protein and a ligand the normal 
procedure would involve several mdrun -rerun runs: (1) with atoms 
charged (2) with the charges on the protein neutralised (3) with the 
charges on the ligand neutralised (4) with the charges on the solvent 
neutralised. When the protein is charged, there will be a net charge in 
the simulation shell in case (2). This net charged is corrected in PME 
as implemented in GMX. In GMX 3.2.1, I could not account for the 
correction, so the calculation wouldn't be exact (see the message 
above). What's the situation in GMX 3.3.1?


Ran Friedman
Laser Laboratory for Fast Reactions in Biology
Department of Biochemistry
Faculty of Life Sciences
Tel-Aviv University
Tel. +972-3-6409824
Fax. +972-3-6409875

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