AMBER Archive (2007)

Subject: Re: AMBER: Solvation net forces

From: David A. Case (case_at_scripps.edu)
Date: Tue Sep 18 2007 - 19:14:55 CDT

On Mon, Sep 17, 2007, Tyler Luchko wrote:
>
> I am implementing an implicit solvation model in Sander called 3D-
> RISM. The solvation forces for each solute atom are integrated off
> of a grid. By looking at several systems we have confirmed that we
> are getting the expected forces except for what appears to be a
> random drift force. I.e. there is a non-zero net solvation force on
> the solute. These forces scale linearly with the number of solute
> atoms and are roughly 0.1 kcal/mol/Angstrom in each direction. I
> would like to simply apply an equal and opposite force to the center-
> of-mass to remove the error.

This looks like a pretty large force error to me. Can you get rid of it
by decreasing the grid size? (Even if this is expensive, it seems like a good
test in order to make sure that there are not other bugs lying around.)

I don't have a particular opinion about subtracting it out, expect that it
*sounds* dangerous....

...regards...dac

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