On Tue, May 02, 2017, Gard Nelson wrote:
>
> The other day, I came across a paper comparing
> the results of several simulation packages.
> (http://link.springer.com/article/10.1007/s10822-016-9977-1) They found
> that the electrostatic energy in AMBER disagrees with other simulation
> packages and suggest that the Coulomb constant in AmberTools may be
> outdated.
I view this is a very minor issue. We could "update" the Coulomb constant
in Amber, but then Amber would still disagree with every other program out
there, just in a different way than it does now; and the entire test suite
and regression tests would need to be carefully examined and updated. And
people trying to reproduce old Amber calculations would face difficulties.
The main advantage to such an update would be to make it slightly easier
to compare results for the "same" force field in different programs. This
is a worthwhile goal, but one that needs widespread community input.
....dac
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Received on Wed May 03 2017 - 11:00:02 PDT
