[gmx-users] PME and coulomb energy calculation

Lei Zhou zhoumadison at gmail.com
Sat Sep 10 23:31:29 CEST 2005

Dear gmx-users,

Recently I have been working on a protein-ligand system and tring to 
determine the coulomb interaction energy between the protein and ligand.
Recently I met a problem closely related with PME and coulomb 
energy analysis.

A protein-ligand was simulated with Gromacs package, with explict 
water, PME for electrostatics and 1.0 nm cutoff. Because gromacs energy 
analysis only give 
the total PME (Coul-LR) for the system, I have to turn off the charges for 
part of the system, rerun the trajectory and then get the Coul-LR (PME 
energy) of protein or ligand or protein-ligand, as suggested by previous 
After that by adding Coul-SR and Coul-LR of protein-ligand, I can get the 
coulomb energy
between protein and ligand.

To double check whether the results is valid, I used a simple program from 
APBS package (coulomb) to calculate the point to point coulomb energy 
between protein and ligand (complex - protein - ligand), using the gromacs 
partial charges.

The results from this two methods are quite consistant from frame to 
frame for the whole trajectory, except there is shift in baseline about 
-1900 KJ/mol. In another words, the difference between those two methods 
is a constant.

I tried to search the gromacs user list and just could not find a clue 
where the difference come from. Is it related to the requirement of PME 
for the total charge of the system to be zero? Since I had to turn 
off the charges of other energy groups to get the Coul-LR (PME energy) of 
a specific group, the net charges of the system is not zero when I 
rerun the trajectory.

I am wondering whether you could give me some suggestions to solve
this puzzle. Thank you.


Lei Zhou
Columbia University, NY
email: lz150 at columbia.edu
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