On Tue, Oct 12, 2010 at 3:19 PM, case <case.biomaps.rutgers.edu> wrote:
> On Tue, Oct 12, 2010, Jason Swails wrote:
>
> > OK, most likely my last post on this topic, as it's not an area I'm
> > particularly enjoying devoting time to. It seems that there is no
> *single*
> > value that I can choose for KB that will make all of the tests pass. I
> put
> > the value that I saw used in runmd.f in constants.f (and subsequently
> > replaced it in all other uses of boltzmann's constant in the src/sander
> > folder). It eliminated a large number of test failures. The only dhfr
> test
> > that does not pass fails with the following, sole diff:
> >
> > possible FAILURE: check mdout.dhfr.dif
> > /Users/swails/newamber/current/amber/test/dhfr
> > 125c125
> > < NSTEP = 9 TIME(PS) = 510.059 TEMP(K) = 298.29 PRESS
> > = 0.
> > ---
> > > NSTEP = 9 TIME(PS) = 510.059 TEMP(K) = 298.28 PRESS
> > = 0.
>
> I could live with this change.
>
> > However, RISM also uses the same constants module, but it actually makes
> use
> > of the constants (i.e. KB) inside, so changing KB to match (most of the)
> > sander test results of course causes small deviations in the RISM tests.
> >
> > The options as I see them: stick with the *most* amber-consistent version
> of
> > the constants and clean up the tests that produce small failures
> (including
> > the RISM tests) OR I can discard everything I've done related to the
> > constants and stick with the status quo. Thoughts are welcome.
>
> I think this sort of thing needs to be attacked at (say) a developers'
> meeting, where everyone can check the changes and discuss the consequences
> in
> person, and real fist-fights can be used to sort out differences of
> opinion.
> If just one person breaks a bunch of tests, everyone points the finger at
> that
> person and stops believing the in the tests. So keep your notes handy, but
> let's revisit this later.
>
That's why I threw my hands up when all of the QM/MM tests started failing.
It's not as simple of a fix as I had previously imagined and sparked a far
more contentious debate than I expected, so I decided to drop it unless
someone picks it back up at the meeting. Far less stressful :).
Thanks,
Jason
> ....dac
>
>
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Tue Oct 12 2010 - 12:30:04 PDT
