[gmx-developers] Excluded charges and PME correction

David van der Spoel spoel at xray.bmc.uu.se
Mon May 3 11:34:46 CEST 2010

On 5/3/10 11:15 AM, Berk Hess wrote:
> If you have exclusions in your topology, the ewald_LRcorrection will
> completely remove
> the mesh electrostatic forces, up to the mesh precision.
> But a single dipole in a box will feel the effect of the periodic images.
> Depending on the size of your box, this can be a large force.

OK, but isn't it strange that this leads to forces perpendicular to the 
dipole as well (the box is cubic)? And shouldn't the dipole correction 
(epsilon_surface != 0) take care of this force?
> Berk
> David van der Spoel wrote:
>> If I have a diatomic molecule with opposite charges, e.g. C=O, which
>> are excluded in the short range, there will be a small force between
>> the atoms due to PME. Is it correct that this force is completely
>> taken away by the routine ewald_LRcorrection?
>> For a simple test system (I2 oriented along the Y axis, with charges
>> +/- 10 and bond length at 0.4 nm) we find at time step zero for bond
>> completely in equilibrium:
>> With cut-off:
>>     f (2x3):
>>        f[    0]={ 0.00000e+00, -2.24787e-03,  0.00000e+00}
>>        f[    1]={ 0.00000e+00,  2.24787e-03,  0.00000e+00}
>> With PME (epsilon_surface = 1)
>>     f (2x3):
>>        f[    0]={ 3.41797e+01, -1.11967e+02,  1.44752e+01}
>>        f[    1]={ 3.41948e+01,  7.41194e+01,  1.44833e+01}
>> With PME (epsilon_surface = 0)
>>     f (2x3):
>>        f[    0]={ 3.41796e+01, -1.73351e+03,  1.44758e+01}
>>        f[    1]={ 3.41922e+01,  1.69567e+03,  1.44829e+01}
>> Surely this can not be correct?
>> This is using the git head sources.

David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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