Dear gmx-users,<br>
<br>
Recently I have been working on a protein-ligand system and tring to <br>
determine the coulomb interaction energy between the protein and ligand.<br>
Recently I met a problem closely related with PME and coulomb <br>
energy analysis.<br>
<br>
A protein-ligand was simulated with Gromacs package, with explict <br>
water, PME for electrostatics and 1.0 nm cutoff. Because gromacs energy analysis only give <br>
the total PME (Coul-LR) for the system, I have to turn off the charges for <br>
part of the system, rerun the trajectory and then get the Coul-LR (PME <br>
energy) of protein or ligand or protein-ligand, as suggested by previous postings. <br>
After that by adding Coul-SR and Coul-LR of protein-ligand, I can get the coulomb energy<br>
between protein and ligand.<br>
<br>
To double check whether the results is valid, I used a simple program from <br>
APBS package (coulomb) to calculate the point to point coulomb energy <br>
between protein and ligand (complex - protein - ligand), using the gromacs <br>
partial charges.<br>
<br>
The results from this two methods are quite consistant from frame to <br>
frame for the whole trajectory, except there is shift in baseline about <br>
-1900 KJ/mol. In another words, the difference between those two methods <br>
is a constant.<br>
<br>
I tried to search the gromacs user list and just could not find a clue <br>
where the difference come from. Is it related to the requirement of PME <br>
for the total charge of the system to be zero? Since I had to turn <br>
off the charges of other energy groups to get the Coul-LR (PME energy) of <br>
a specific group, the net charges of the system is not zero when I <br>
rerun the trajectory.<br>
<br>
I am wondering whether you could give me some suggestions to solve<br>
this puzzle. Thank you.<br>
<br>
Sincerely,<br>
<br>
Lei Zhou<br>
Columbia University, NY<br>
email: <a href="mailto:lz150@columbia.edu">lz150@columbia.edu</a><br>