Dear Dave,
Recent changes in pbsa is to make sure the code is consistent with the manual. In Amber 11, we kept a lot of keywords backward compatible and in this release, they are either phased out or changed to optimal value that have been tested extensively and published, such as cavity_surften and cavity_offset. We're sorry we did this late but it's a necessary move. In the next few days, you'll probably see more updates on the code and test cases for the above purpose. Of course we'll test all before we push.
Thanks,
Qin
On Mar 4, 2012, at 6:20 AM, case wrote:
> 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.
>
> ----------------------------------------------------------------------------
> 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.]
>
> ----------------------------------------------------------------------------
>
> 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.
>
> ----------------------------------------------------------------------------
>
> ...thanks....dave
>
>
>
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Received on Mon Mar 05 2012 - 13:30:02 PST
