AMBER Archive (2006)

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

From: Lwin, ThuZar (ThuZar.Lwin_at_stjude.org)
Date: Fri Aug 04 2006 - 14:02:10 CDT

Dr. Case,
   Thank you.
   In my disappearing vdw simulations,1-4 EEL is indeed zero. In my
charging simulation in solvent, I happened looking up the md.output file
of
clambda=0.5. So that's why 1-4 EEL is not zero yet.

Thank you,
ThuZar

-----Original Message-----
From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf
Of David A. Case
Sent: Friday, August 04, 2006 11:19 AM
To: amber_at_scripps.edu
Subject: Re: AMBER: question on chargning free energy in solvent vs
vacuum. .

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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