Re: long range electrostatics for alchemical transformation

From: nmichaud_at_jhu.edu
Date: Thu Aug 17 2006 - 20:38:13 CDT

Do you know how they accomplish this? As far as I can tell, the only way
to do this with the the mesh based methods requires three FFTs, one for
each group-environment interaction (only projecting the group and the
environment onto the grid), and then you have to subtract
the contribution of the environment with itself (since it was
double-counted). Is this what NAMD does?

Naveen

---------------------------------------------------------------------
Naveen Michaud-Agrawal
Program in Molecular Biophysics
Johns Hopkins University
(410) 614 4435

On Thu, 17 Aug 2006, Richard Wood wrote:

> I believe that the two alchemical groups don't see each other, and that
> interactions are calculated within each "structure" as it were.
>
> Richard
>
>
> Richard L. Wood, Ph. D.
> Computational Chemist
> Cockeysville, MD 21030
> rwoodphd_at_yahoo.com
>
> ----- Original Message ----
> From: nmichaud_at_jhu.edu
> To: namd-l_at_ks.uiuc.edu
> Sent: Thursday, August 17, 2006 3:36:44 PM
> Subject: namd-l: long range electrostatics for alchemical transformation
>
>
> I have a question about how long-range electrostatics are handled during
> an alchemical transformation. How does NAMD treat the interactions of the
> two alchemical groups with the images of the other group. Does NAMD
> remove the contribution from the images of the created group on the
> abolished group and vice versa? Thanks.
>
> Naveen
>
> ---------------------------------------------------------------------
> Naveen Michaud-Agrawal
> Program in Molecular Biophysics
> Johns Hopkins University
> (410) 614 4435
>
>
>
>
>

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