[gmx-developers] Excluded charges and PME correction

David van der Spoel spoel at xray.bmc.uu.se
Mon May 3 11:10:59 CEST 2010

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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