[gmx-developers] ewald shift

Rossen Apostolov rossen at cbr.su.se
Sat Aug 15 22:13:20 CEST 2009


You might want to check the Fennell potential method, which is an
extension of Wolf and improves the force discontinuity at cutoff:
Fennell, C. J.; Gezelter, J. D. J Chem Phys 2006, 124, 234104 and
Kikugawa et al., J Comput Chem. 2009 Jan 15;30(1):110-8.

Another alternative you might want to try is the isotropic periodic sum
method, Wu X, Brooks BR,  J Chem Phys. 2005 Jan 22;122(4):44107. You
should be careful though if you use it to simulate interfaces.


Harold Park wrote:
> Hi Berk:
> My apologies for posting on the same list.  Regarding the utility of
> the Wolf paper - it does not artificially truncate the Coulomb
> interactions at a cut-off.  It does use a spherical cut-off radius,
> but then it corrects the Coulomb energy by ensuring charge
> neutralization.  Doing so leads to a very simple expression for the
> Coulombic energies (equation 5.10) and forces (equation 5.21).  In
> that way, the Coulombic energy (and thus forces) can be calculated
> exactly using spherical truncation, as is often used in MD
> simulations, with a small cut-off radius.
> I am aware that there are other methods that are used for non-periodic
> systems in slab geometries, but the Wolf method is general, and thus
> not utilize arguments to make the slab non-periodic in certain
> directions, while using Ewald in the other periodic directions.  In
> contrast, the Wolf method can be used both at surfaces and for bulk
> systems.
> Regards,
> Harold
>> -- 
>> Message: 1
>> Date: Fri, 14 Aug 2009 16:36:05 +0200
>> From: Berk Hess <hess at cbr.su.se>
>> Subject: Re: [gmx-developers] ewald shift question
>> To: Discussion list for GROMACS development
>>     <gmx-developers at gromacs.org>
>> Message-ID: <4A857655.9090009 at cbr.su.se>
>> Content-Type: text/plain; charset=ISO-8859-1
>> Hi,
>> 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
>> (ewald_geometry=3dc)
>> which works very well and there are also exact methods in the literature
>> for this geometry.
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