Re: AMBER: Solvation net forces

From: Tyler Luchko <>
Date: Tue, 25 Sep 2007 13:21:24 -0600

On 18-Sep-07, at 6:14 PM, David A. Case wrote:

> 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.)

Yes, decreasing the grid spacing by 50% does make a difference and
the drift force comes down to 4e-3 kcal/mol/angstrom per atom.
However, this adds considerable cost in terms of memory and time.
Decreasing the grid spacing again by 50% gives a drift error of 2e-3
kcal/mol/angstrom per atom.

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

I agree, it does sound dangerous, which is why I am interested in
other opinions.

In Essman et al., J. Chem. Phys., 103, 8577 they state that the net
force on the atoms calculated from PME is not zero and on the the
order of the RMS error in the force. In particular they suggest
removing the average net force from each atom to avoid a slow
Brownian drift about the centre of mass. If this is an acceptable
approach I would like to know what is an acceptable drift error to
subtract off.

Thank you,


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Received on Wed Sep 26 2007 - 06:07:23 PDT
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