[gmx-developers] ewald shift question

Berk Hess hess at cbr.su.se
Fri Aug 14 16:36:05 CEST 2009


Please do not post the same question on multiple lists.
People might answer the same questions multiple times and the discussion
gets confusing.

You can simply call shift_LRcorrection if you want, right?
Also ewald_LRcorrection does nearly the same thing, but with a different
functional shape.
Both function are called at nearly the same place in do_force_lowlevel
in src/mdlib/force.c.

But having looked quickly trough the paper, it would think that you
don't need these functions
at all.  You want to shift the pair potential for all pairs, or am I wrong?
Both functions in Gromacs only operate on excluded pairs.
Shifting a pair potential can be done simply with user tables.

BTW I don't see the advantage of this electrostatics method.
Artificially truncating all Coulomb pair interactions at a cut-off is
exactly the same
as using a pure cut-off (although this method is probably
computationally more efficient).
I would consider the artifacts due to this worse than the artificial
periodicity introduced by
Ewald and PME.
For interface systems Gromacs has a correction term for Ewald and PME
which works very well and there are also exact methods in the literature
for this geometry.


Harold Park wrote:
> Dear Gromacs Developers:
> My student and I are currently trying to use Gromacs 4.0.5 to perform
> some electrostatic analysis of nanostructures.  One of our goals is to
> implement the method of Dieter Wolf et al. (D. Wolf, P. Keblinski,
> S.R. Phillpot and J. Eggebrecht, Journal of Chemical Physics 1999;
> 110:8254-8282) to calculate the Coulombic energy for ionic systems,
> such that the periodicity assumptions inherent in the Ewald-type
> approaches can be avoided.
> In older versions of Gromacs, it appeared that there was a
> shiftLR_correction implemented as one option to calculate the
> Coulombic energies.  However, in 4.0.5, we have found code in
> ewald_util.c and ewald.c which should correspond to that for
> shiftLR_correction, but we find that these functions are not actually
> called when using the shiftLR_correction option.  Modifying the
> shiftLR_correction option is the best for us since the functional
> forms of the Coulomb energy in the Wolf method is quite similar to these.
> Thus, I was wondering:
> (1) Is the shiftLR_correction option obsolete in Gromacs 4.0.5?
> (2) If so, what would be the best way to implement a new Coulombic
> energy and force calculation approach (i.e. that of Wolf et al.) into
> Gromacs?
> Harold Park
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