[gmx-developers] ewald shift question
hess at cbr.su.se
Fri Aug 14 16:36:05 CEST 2009
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You can simply call shift_LRcorrection if you want, right?
Also ewald_LRcorrection does nearly the same thing, but with a different
Both function are called at nearly the same place in do_force_lowlevel
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
> Harold Park
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