I'm not even remotely an expert on belly or Ewald, but isn't there a warning
printed when using them together that states that the calculations are not
formally correct? Presumably you have explained exactly why this is so,
although I think it also states that things will be "mostly correct" as far
as brief minimizations and such go.
My understanding was that standard AMBER practice is to eschew use of belly.
Brian
On Thu, Jul 28, 2011 at 3:48 PM, Ignacio J. General <ijgeneral.gmail.com>wrote:
> Dear Amber users:
>
> After experimenting a little with Belly using Ewald, I found something
> I didn't expect about the MD output energies. Could anybody please
> check that what I understand is correct?
>
> In the standard output there are, among several other quantities, one
> called EELEC and another called 1-4EEL. The 1st one gives the total
> Ewald electrostatic energy of the system, with the exception of the
> 1-2, 1-3 and 1-4 interactions (or are those terms also included?). The
> 2nd one gives a 1-4 electrostatic energy, calculated outside Ewald, I
> imagine in the same way that the others (BOND, ANGLE, etc.) are
> calculated. So that if you put together EELEC + 1-4EEL, you get the
> total electrostatic energy of the whole system (of course, except 1-2
> and 1-3 interactions).
>
> So far, so good. But I found out that if you use belly, then the
> 1-4EEL (along with BOND, ANGLE, etc.) ignore the energies between
> fixed atoms. On the other hand, the Ewald calculation, and thus EELEC,
> is unaffected by belly, so that energy does include even the fixed
> atoms. So EELEC and 1-4EEL are incompatible! Consequently, if we do
> EELEC + 1-4EEL, we don't get the total electrostatic energy of the
> system.
>
> This could not be a problem, depending on what you are calculating. In
> particular, if you do charge TI, DV/DL is obtained from (EELEC +
> 1-4EEL), so you may have big problems here...
>
> If anybody has some comment on this I would really appreciate it.
>
> Ignacio
>
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>
--
================================ Current Address =======================
Brian Radak : BioMaPS
Institute for Quantitative Biology
PhD candidate - York Research Group : Rutgers, The State
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Received on Thu Jul 28 2011 - 13:00:11 PDT
