[gmx-developers] Excluded charges and PME correction
Berk Hess
hess at cbr.su.se
Mon May 3 14:54:51 CEST 2010
David van der Spoel wrote:
> On 5/3/10 11:39 AM, Berk Hess wrote:
>> David van der Spoel wrote:
>>> 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?
>> It all depends on your box matrix and PME accuracy settings.
>> The dipole correction never fully takes care of this, it simply reduces
>> it by 1/epsilon.
>> The 3dc geometry will remove most of it, but not everything.
>>
>> I guess the perpendicular forces should be (close to) zero, unless your
>> box is triclinic.
> It seems that it is worse, forces are position-dependent. If my
> molecule is in the center of a cubic box of 2 nm I get the
> perpendicular force close to zero (step 0):
> x (2x3):
> x[ 0]={ 1.00000e+00, 1.20000e+00, 1.00000e+00}
> x[ 1]={ 1.00000e+00, 8.00000e-01, 1.00000e+00}
> v (2x3):
> v[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
> v[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
> f (2x3):
> f[ 0]={ 0.00000e+00, 3.17667e+03, 8.47711e-04}
> f[ 1]={-2.28882e-03, -3.17667e+03, -8.47711e-04}
>
> If I change the grid spacing from 20 (0.1 nm) to 21
> f (2x3):
> f[ 0]={-4.50611e-03, 3.12076e+03, 6.21270e-03}
> f[ 1]={-5.40733e-03, -3.12078e+03, 2.74640e-03}
>
> to 22
> f (2x3):
> f[ 0]={ 6.34670e-03, 3.37936e+03, 0.00000e+00}
> f[ 1]={ 2.51770e-03, -3.37933e+03, 0.00000e+00}
>
> to 23
> f (2x3):
> f[ 0]={-3.29018e-03, 3.05586e+03, 5.31634e-03}
> f[ 1]={ 1.07188e-02, -3.05586e+03, 5.31634e-03}
>
> Now if I move the coordinates by 0.3 nm in the X-direction I get:
> f (2x3):
> f[ 0]={-3.65754e+01, 3.04537e+03, -4.07583e-04}
> f[ 1]={-3.65607e+01, -3.04536e+03, -4.07583e-04}
>
> Or by 0.5 nm in X:
> f (2x3):
> f[ 0]={ 8.38358e+01, 3.05105e+03, 1.18744e-03}
> f[ 1]={ 8.38223e+01, -3.05105e+03, 1.18744e-03}
>
> Or by 05 nm in X and 0.5 nm in Z:
> f (2x3):
> f[ 0]={ 8.38596e+01, 3.04622e+03, 8.38235e+01}
> f[ 1]={ 8.38329e+01, -3.04621e+03, 8.38232e+01}
>
>
> So the force in the Y direction depends on grid spacing and in X and Z
> on the position.
> As you see, the above force will lead to a net translation.
>
>
Can you post the box and all PME parameters?
These are all things I would expect, but the magnitude depends on your
settings.
Berk
More information about the gromacs.org_gmx-developers
mailing list