AMBER Archive (2006)

Subject: Re: AMBER: question on chargning free energy in solvent vs vacuum

From: David A. Case (case_at_scripps.edu)
Date: Fri Aug 04 2006 - 11:18:53 CDT

On Thu, Aug 03, 2006, Lwin, ThuZar wrote:
>
> But when I simulate the system in solvent, the EELEC and 1-4 EEL terms
> are no longer zero (even though I have set the charges of the atoms on
> toluene to zero).

I agree that this sounds suspicious, but can't really say more. Are you sure
that the charges are zero in both states? My toluene -> nothing runs (i.e.
where the charges are already zeroed and I am just changing the vdW radii)
indeed show 1-4 electrostatics as zero, as expected. So you should check
carefully you results: run a short simulation at both lambda=0 and lambda=1 to
make sure the end points are doing what you expect, etc.

...good luck...dac

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