[gmx-users] Coulomb-LR for single ion with PME

Steven Spronk spronk at its.caltech.edu
Sat Apr 23 02:07:49 CEST 2005

Hello everyone,

I realize that this topic has come up on the list several times before,
but I'm still not able to put it all together.  I am interested in
calculating the coulombic energy between a single ion and the rest of the
system, which requires some tricks, since I'm using PME.

After reading previous posts, I still had these questions:

1)  Should I turn off the dipole energy correction (and if so, I assume I
should turn it off in both energy calculations: the total energy as well
as the system-system energy)?


2)  Specifically, what do I have to do with the charge energy correction
to get meaningful energies?  Do I have to go into the ewald_util.c code
and take out the correction term, which is what I think I understand from

I understand that PME gives only a single value for the long-range energy
that cannot be broken down into groups.  I need to use tpbconv to make a
new tpr file that neutralizes the charge, and then performing mdrun -rerun
will give me the coulombic energy of the system with itself.  The
difference between these two energies is the number I'm looking for.

On previous posts to this list, there was concern over the fact that
neutralizing the charge of a single ion will result in a system that has a
charge, which of course isn't so good for PME.  People were directed to
check the charge energy correction, and the dipole energy correction was
also mentioned.  But I couldn't find the exact steps that I need do.

Thanks a lot!

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