Hi David,
I'll try to study the code to see how amber corrects the 1-2, 1-3 and 1-4 Coulomb interactions for PME.
Best,
Shenglong
On Dec 19, 2012, at 7:56 AM, David A Case <case.biomaps.rutgers.edu> wrote:
> On Tue, Dec 18, 2012, Shenglong Wang wrote:
>>
>> Thanks a lot for the idea. I have another question, if I just simply
>> substrate Coulomb interactions, how to deal with the cutoff issue? For
>> Ewald sum or PME, there is cutoff for the short range interactions
>> in the real space, how to match this cutoff with the one for Coulomb
>> interactions between these two groups of atoms?
>
> I don't understand the question, but will give a couple of notes that might be
> relevant:
>
> 1. The Coulomb "cutoff" in PME can be thought of as a (hidden) internal detail
> of the implementation: you can change the cutoff with effectively no change in
> the interactions. There's nothing physical there.
>
> 2. The only consistent way I can think of (offhand!) to modify the Coulomb
> interaction is to define the modified interaction to exist among a fixed set
> of atoms, with no cutoffs based on distance. Then you can subtract a fixed
> number of Coulomb terms, and add back in the same number of modified
> interaction terms.
>
> 3. You probably should study the code to see how 1-2, 1-3 and 1-4 electrostatic
> interactions are handled, since this sounds just like what you propose. That
> is: 1-2 interactions have a "modified Coulomb interaction" (which happens to
> be zero), and 1-4 interactions have a scaled Coulomb interaction. In each
> case, the code subtracts out the unmodified Coulomb interaction and adds back
> in the modified one.
>
> ....dac
>
>
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Received on Wed Dec 19 2012 - 06:30:03 PST
