On 03.03.12, case wrote:
> On Sat, Mar 03, 2012, Holger Gohlke wrote:
> >
> > with a new "pull" from origin/master, the problem due to sander in the
> > decomposition of mm_pbsa.pl is gone. Thanks to whoever solved this.
>
> I'd like more information, please:
>
> 1. What is your latest commit from git?
These were my last two actions with git today:
commit 23df75b9a36f3d1fceedc94be921f94776c96ffa
Merge: 25f18c2 84b2097
Author: Holger Gohlke <gohlke.hhu.de>
Date: Sat Mar 3 13:37:41 2012 +0100
Merge branch 'master' of git.ambermd.org:amber
commit 25f18c2ef382b739df260d75e11c1beee753f587
Author: Holger Gohlke <gohlke.hhu.de>
Date: Sat Mar 3 13:35:52 2012 +0100
Updated example 11 of mm_pbsa.pl now using the latest iAPBS version available within APBS1.3.
> 2. Can you define what you mean by "the problem due to sander in the
> decomposition of mm_pbsa.pl is gone"?
We had observed a problem with the decomposition of internal(!) energies in $AMBERHOME/src/mm_pbsa/Examples/05_MMPBSA_Decomp_Residue. This is gone now.
> All of the test cases still seem to
> fail, and the differences (e.g. in the "idecomp1" test directory)
> show differences in the surface area terms, not in the polar parts.
In $AMBERHOME/src/mm_pbsa/Examples/05_MMPBSA_Decomp_Residue, the differences arise from the PB polar part whereas the surface part from GB agrees.
>
> So: what is it that now works that didn't work before?
See above: internal energy decomp in 05_MMPBSA_Decomp_Residue works again.
> Do we have any way
> to know at all what change to sander we are talking about?
>
> And, how can we figure out what is a "good result" for the test cases? Is
> there a way to recover the PB settings that were used for Amber11?
>
> Maybe if everyone could focus on just the idecomp1 test, that would help.
>
> What I see it that the current code gives identical answers for all the
> EGB terms, but divergent answers for the ESURF and related terms. [This
> is at odds with the behavior reported by Holger, so we need details from
> him.] Most of the ESURF diffs are small (which is why I thought they
> might of come from new radii), but at lines 511 and 518 there are enormous
> diffs (thousands of kcal).
>
> If anyone has the time, you could start from the "olderDusseldorf" branch
> that James put together. This has the code before the Feb. 3 changes from
> Dusseldorf, plus the changes James made during February. I believe that the
> head of this branch passes the idecomp1 (and other decomp) tests. We need
> to cherry-pick one-by-one the Dusseldorf Feb. 3 changes, plus all the Irvine
> changes, to try to locate the origin the test failure.
>
We will compare our current version against the olderDusseldorf branch, also looking at idecomp1.
Best regards
Holger
>
> Let's try to make this a true regression test: find parameters for the current
> code that will give the same numerical answers as with Amber11, [or be *sure*
> we understand why the earlier answers were wrong.]
>
> ...thanks...dave
>
>
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--
++++++++++++++++++++++++++++++++++++++++++++++++++
Dr. Holger Gohlke
Professor fuer Pharmazeutische/Medizinische Chemie
Heinrich-Heine-Universitaet Duesseldorf
Institut fuer Pharm. und Med. Chemie
Universitaetsstr. 1
40225 Duesseldorf
Germany
Tel.: (+49) 211-81-13662; Fax: (+49) 211-81-13847
Email: gohlke.uni-duesseldorf.de
URL: http://cpclab.uni-duesseldorf.de
++++++++++++++++++++++++++++++++++++++++++++++++++
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Received on Sat Mar 03 2012 - 16:00:01 PST
