There are two issues in this email: one regarding recent changes in the PB
codes, the second regarding changes to icosasurf and decomp in sander.
Qin and Ray should look at the first one, Holger and Nadine at the second.
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On Sun, Mar 04, 2012, Holger Gohlke wrote:
> I forward an email from Nadine regarding the pbsa / decomp issue. Would
> this be a starting point for further searching?
>
>
> we re-checked the differences in the polar solvation energy. We
> observed differences in all mm_pbsa/Examples test runs, in which the
> solvation free energy is calculated with the PBSA module. For the
> hybrid model test and the decomposition analyses the differences in PB
> energy were especially large. According to our investigations these
> differences were introduced by changes made between 27.02.2012, 5:35
> pm (8ad8c24ef9016553bcc3e9830bb3aac040877873) and 03.03.2012, 1:37 pm
> (23df75b9a36f3d1fceedc94be921f94776c96ffa).
Thanks for the information. My current guess is that these were made by
changes in the default PB parameters. If so, it is important to find out
if there is a way to get Amber12 to give the same PB output as Amber11 gave.
[Also, if Amber12 is giving significantly different results by default than
Amber11, do we understand why? Are the new results supposed to be "better"
than the old ones? It is rather disconcerting that we are seeing changes in
PB behavior so very, very late in the development cycle. As a reminder,
distributed code is supposed to be code that groups are actually using for
research. It is not supposed to represent the latest ideas that might seem
good but haven't been tested much.]
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In addition to the changes in mm_pbsa_Examples, there have been
changes in the sander "decomposition" tests. In particular, the "idecomp1"
test uses GB (not PB), so problems there are (probably) unrelated to changes
in the PB code. These test cases look like they started to fail near the
beginning of Feb. Specifically, the following two commits appear to have
changed the idecomp1 test output:
commit 8d206b3848de52d17549055b948848b1c1e558a9
Author: Holger Gohlke <gohlke.hhu.de>
Date: Fri Feb 3 14:41:25 2012 +0100
Bugfix of initialization in icosa_init
commit 6ac8353095b0adc12119a23193ffc7d29382d28d
Author: Holger Gohlke <gohlke.hhu.de>
Date: Fri Feb 3 14:41:52 2012 +0100
Bugfix to ensure backward compatibility for ICOSA surface calculation to
Amb
[I cherry-picked these into the olderDusseldorf branch: before, the tests
pass; afterwards they failed. -- note: just "make sander" in that branch,
then "mv sander ../../bin" in order to run the tests.] So, Holger and Nadine
should carefully revisit the above commits.
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...thanks....dave
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Received on Sun Mar 04 2012 - 06:30:02 PST
