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?
2. Can you define what you mean by "the problem due to sander in the
decomposition of mm_pbsa.pl is gone"? 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.
So: what is it that now works that didn't work before? 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.
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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Received on Sat Mar 03 2012 - 15:00:02 PST
