On Mon, Oct 11, 2010, Thomas Cheatham III wrote:
>
> To date we have not held to a gold standard; in fact, the current lead
> (i.e. Pb) standard for a particular force field that we have applied
> to-date is code snapshot, run-time options, methods, and implementations
> used *at* the time the force field was developed.
I'll just note that the energies for the main DHFR test case (in
$AMBERHOME/test/dhfr/mdout.dhfr.save) have remained the same to all printed
digits (about 9 significant figures) since Oct. 8, 2001. That was when we
went from the "pure" leapfrog integrator to what is essentially velocity
verlet for estimating kinetic energies.
The potential energies haven't changed since (at least) March 1999, which is
as far back as the current git repo tracks things. That was at Amber6, when
(as I remember) we went to the current smooth PME implementation. I'm pretty
sure (tm) that Amber 5 had slightly different energies, traceable to a
slightly different PME implementation.
Since this is an NVE simulation, I don't think that changing pconv
should affect it, but I agree with Tom that one should be very careful
in changing constants by tiny amounts just for the sake of changing
constants. The dhfr results, in particular, are de facto "correct", having a
decade or so of use both in our test suites and as the "jac" benchmark that
everyone now sees in NVIDIA clips.
[I know that a few hours ago I recommended updating the test cases, but
I've changed my mind, at least about some key NVE test cases; some of the
key GB tests like gb_rna should probably also remain unchanged. Also, I'm
not counting formatting changes here, which *have* happened for dhfr.]
....dac
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Received on Mon Oct 11 2010 - 20:30:03 PDT
