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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--
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 - 19:30:06 PST
