[gmx-users] Coulomb-LR for single ion with PME
spoel at xray.bmc.uu.se
Sat Apr 23 08:57:16 CEST 2005
On Fri, 2005-04-22 at 17:07 -0700, Steven Spronk wrote:
> 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.
In the CVS version of gromacs there is new program src/contrib/pmetest.c
that does print out the different contributions (including the
correction terms). It does not yet automatically compute all the
interactions between groups. In tests that I did the Ewald correction
for a charged system was very small, but please test it yourself.
> Thanks a lot!
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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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