[gmx-users] [Fwd: questions about PME and Coulomb energy]

David spoel at xray.bmc.uu.se
Sun Sep 11 16:06:15 CEST 2005

-------- Forwarded Message --------
From: lz150 at columbia.edu
To: spoel at xray.bmc.uu.se
Subject: questions about PME and Coulomb energy
Date: Sun, 11 Sep 2005 09:28:02 -0400
Dear Prof. Spoel,

Sorry for directly sending the email to you. I sent an email to
gromacs email list but haven't hear any answers yet.

Recently I have been working on a protein-ligand system and tring to
determine the coulomb interaction energy between the protein and
ligand. I got some strange difference comparing the energy
calculated by Coulomb (with APBS/tools/manip) and by PME in
gromacs. Could you give me some suggestions about a strange problem?

The protein-ligand system was simulated with Gromacs package, with
explict water, PME for electrostatics and 1.0 nm cutoff. Because
gromacs energy 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 you and other people.
After that by summing Coul-SR and Coul-LR
of protein-ligand, I can get the coulomb energy between protein and

To double check whether the results is valid, I used the Coulomb
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 pqr file was generated
automatically by editconf from gromacs (with -mead option on).

The results from this two methods are very 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 for the whole trajectory and that is
determinded by some intrinsic properties of the protein.

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.

Or the PME result is more reliable in terms of treating long term
energies? Or is this related with the periodicity of PME mentioned
some papers, since with Coulomb from APBS I have only one protein
and one ligand, but for gromacs I used PBC?

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


Lei Zhou
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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