[gmx-users] amber99sb in GROMACS vs amber99sb in AMBER

Michael Shirts mrshirts at gmail.com
Mon Nov 21 21:21:37 CET 2011

> Is anyone aware of any benchmark analysis about the implementation of the
> amber99sb force field (or any of its variants: 99sb-ildn, 99sb-nmr) in
> GROMACS and AMBER. I am interested to know in what extend the energies
> correlate and if the results agree with experimental data.

Whether the results compare agree with experimental data is irrelevant
to the correctness of the implementation -- that has to do with the
validity of AMBER99sb to begin with.  The only question is, do GROMACS
and AMBER give the same energies for the same configurations?

I actually do not know the answer, and would be interested to hear if
it's been tested.  http://ffamber.cnsm.csulb.edu/ does not appear to
have the very comprehensive tests that appear for earlier models at
the current time.  I SUSPECT there should not be a problem, since
AMBER99sb just changed a couple of torsions, so errors are unlikely
(though in theory possible).

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