Re: [AMBER-Developers] significant recent tleap changes

From: Ross Walker <>
Date: Fri, 11 Nov 2011 15:55:27 -0800

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

|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
| Adjunct Assistant Professor |
| Dept. of Chemistry and Biochemistry |
| University of California San Diego |
| NVIDIA Fellow |
| | |
| Tel: +1 858 822 0854 | EMail:- |

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Received on Fri Nov 11 2011 - 16:00:03 PST
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