[gmx-developers] high-precision TIP3P parameters?

Erik Lindahl erik.lindahl at gmail.com
Mon May 29 09:45:37 CEST 2017


I think Igor has a point that we should make our implementation of Amber as
accurate as possible, but let's make sure we only change things once.

There has also been at least once instance where Amber changed they way
they defined improper torsions internally without documentation, so we went
from perfect matches in Amber ~8 to mismatching, and then back to matching.

1. I agree the Amber implementation should be our reference for Amber, but
do the parameter files in the Amber package match the published force field
exactly? Let's double-check that paper.

2. This If we should change, I would suggest making a quick audit of _all_
our Amber parameters and see if there are more rounding errors/deviations.
If so, let's change all of them at the same time.

3. I also agree with Berk that this is only worth doing if we really get
everything to match pretty close to perfectly. It's better to have a known
insignificant discrepancy than a set of parameters that keeps changing!



On Mon, May 29, 2017 at 9:36 AM, Berk Hess <hess at kth.se> wrote:

> Hi,
> My opinion is that we should minimize the number of time we change force
> field parameters, as this is confusing for users. The difference here is
> very small and the Coulomb constant also differs from Amber. I would only
> want to change this when we can get the total energy to match the Amber
> code up to all decimals.
> Cheers,
> Berk
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Erik Lindahl <erik.lindahl at gmail.com>
Professor of Biophysics, Dept. Biochemistry & Biophysics, Stockholm
Science for Life Laboratory, Box 1031, 17121 Solna, Sweden
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