Thanks!
I already reverted the changes to leap. Tried to revert changes I made to
sander, but can't do it. There is already conflict. But the sander code
passed the test suite before I committed.
yong
On 11/11/11 7:25 PM, "Jason Swails" <jason.swails.gmail.com> wrote:
>On Fri, Nov 11, 2011 at 10:22 PM, Yong Duan <duan.ucdavis.edu> wrote:
>
>>
>> Ross, please revert commits for me:
>>
>> 4c55708c8daabd3289ac4558889849d756532edc
>>
>> e7290894585886f8af70a7f64363139b6bdf4a35
>>
>> I am unfamiliar to git and don't want to mess up further. Please do it
>>for
>> me. Thanks!
>>
>
>No need for that, I don't think. Outside of the one issue I mentioned
>above, the topology files are identical to the post-14-scaling-version of
>tleap from AT1.5. There should be a way of determining which dihedrals
>are
>impropers (and subsequent terms of a normal dihedral) and just set those
>to
>0 without having to revert all of your changes.
>
>Thanks!
>Jason
>
>
>>
>>
>> yong
>>
>> On 11/11/11 3:55 PM, "Ross Walker" <ross.rosswalker.co.uk> wrote:
>>
>> >Hi Yong,
>> >
>> >> Improper 1-4's are never used, either in sander or in pmemd. I am not
>> >> sure
>> >> in other programs, hopefully consistent. Putting 0's is fine. I can
>> >> update
>> >> that.
>> >
>> >What you mean is 1-4 impropers do not feature in the code that
>>calculates
>> >1-4 VDW and EEL I assume? - Certainly they are used in the dihedral
>>code.
>> >
>> >Note the 0's should NOT just be there for the impropers. They should be
>> >there for ALL additional dihedrals. This is a safety check. The code
>> >should
>> >only calculate a 1-4VDW / EEL for the first dihedral in a set it gets
>>to.
>> >Having the additional dihedrals have scaling factors of 0 means if
>>someone
>> >messes with things, and puts dihedrals out of order, messes up the
>>section
>> >that labels unique dihedrals etc then you get infinity and the code
>> >crashes
>> >rather than just silently producing junk.
>> >
>> >Thus I would make sure things match properly here with older code.
>> >
>> >> Besides these "failures", you will also see CMAP-related failures.
>>Both
>> >> sander and pmemd can take CMAP without CHARMM option.
>> >
>> >Why have all the test cases not been updated along with the checkin???
>> >
>> >> This means the test suite needs to be updated and that the "new" test
>> >> suite will cause a lot of "failures" to the old code and vice versa.
>> >
>> >I always assume updating the test cases (not just replacing the saved
>> >output
>> >but replacing them with results you know to be correct and have
>>carefully
>> >tested by hand) is a key part of checking in updated code. If you don't
>> >include test cases and updated test cases with your code checkins then
>>the
>> >code should NOT be being checked in.
>> >
>> >Note, once I have cruise control up and running properly running all
>>the
>> >test cases on a regular basis if you check something in that breaks the
>> >test
>> >you will be getting regular emails from the git server politely
>>informing
>> >you of your 'mistake'.
>> >
>> >All the best
>> >Ross
>> >
>> >
>> >/\
>> >\/
>> >|\oss Walker
>> >
>> >---------------------------------------------------------
>> >| Assistant Research Professor |
>> >| San Diego Supercomputer Center |
>> >| Adjunct Assistant Professor |
>> >| Dept. of Chemistry and Biochemistry |
>> >| University of California San Diego |
>> >| NVIDIA Fellow |
>> >| http://www.rosswalker.co.uk | http://www.wmd-lab.org/ |
>> >| Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
>> >---------------------------------------------------------
>> >
>> >Note: Electronic Mail is not secure, has no guarantee of delivery, may
>>not
>> >be read every day, and should not be used for urgent or sensitive
>>issues.
>> >
>> >
>> >
>> >
>> >
>> >
>> >_______________________________________________
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>>
>>
>>
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>
>
>
>--
>Jason M. Swails
>Quantum Theory Project,
>University of Florida
>Ph.D. Candidate
>352-392-4032
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Received on Fri Nov 11 2011 - 21:00:03 PST
