Re: [AMBER-Developers] Ground rules for discussion of Amber12

From: Ken Merz <>
Date: Sat, 5 Nov 2011 12:00:57 -0400


 I second Dave's rule setting. Some of the exchanges were getting too heated for my tastes.

 A few years ago I read an article that described studies on e-mail lengths and impact. If an e-mail got longer than the typical reader screen (say 20-30 lines) their impact decreased dramatically. People just don't read them. I have to admit that slugging through some of these e-mails has been very painful. Hence, Dave's second point is very germane.

 There have also been comments about professional software development. I am not sure how many of us have actually worked in a professional software dev operation, but I have. While at Accelrys I ran such a group and believe me (in my opinion) it truly sucked. We had endless meetings discussing what we would code and then we would code it, pass it along to a QA/QC group that would rip it to shreds and then meet again to decide how to fix things before we even laid finger to keyboard. Don't even get me started on the support and marketing side of this as well. Is this what we want for AMBER? Gosh, I hope not!

 Finally, comparing our merry band of adventurers to Amazon, which is a multi-billion dollar company or even Baker's lab that has millions in HHMI money is not really the best analogy to our situation. We have significantly less resources than these operations, which we could increase, but it will take a lot of effort to convince the NIH, for example, to help us out.

 Maybe I have already violated the 20-30 line rule, so sorry in advance.

 Enjoy the rest of the weekend!

 Take care, Kennie

On Nov 4, 2011, at 11:28 PM, case wrote:

> I'm happy to see so much interest and passion about how to make Amber better,
> but we need some ground rules, before productive discussions become
> flame wars:
> 1. Please don't post things that can be construed as attacks of other
> developers. Go out of your way to be polite, and edit your posts (before
> hitting "send") with this in mind.
> 2. Keep your posts short and on-topic. It helps to see the gist of
> ideas for making things better, but at this stage the details of the
> implementation can be a distraction. If you really need a lot of space,
> use an attachment to hold the details.
> 3. I think the general outline of what will happen with Amber12 is actually
> pretty clear, and doesn't involve radical changes:
> a. AmberTools will still exist (because people are used to it, and because
> a growing number of projects outside of Amber make use of it.)
> b. Amber will still exist, as a paid-for entity, but our goal is to make
> the combination of Amber+AmberTools as useful as possible to ourselves
> and to the community, not to maximize the revenue we receive.
> c. I'm leaning towards keeping sander as a part of Amber. It would be
> considerably simpler to move it to AmberTools (as Jason, Tyler,
> Taisung and I have argued), but this might represent a bigger change
> than we want to tackle right now. Comments on this item are welcome
> (consistent with points 1 and 2 above), but mainly from those who
> have not already weighed in on this topic before.
> d. We can take useful steps to simplify the building and testing of our
> codes. A lot of this can be done by improving the Makefiles and scripts
> we already have. Jason has some good ideas about how to manage bugfixes
> and updates. Bigger changes (cmake might be an example) can be
> considered, but time is short.
> e. Having a bias toward reducing the number of separate programs is fine,
> but each project is different, and I don't see us changing from offering
> a "package of molecular simulation programs" that work reasonably well
> together. It's unfortunate but probably telling that (aside from
> Romain) we've not had a single comment about improving the documentation
> or the tutorials. Limitations there are probably more harmful to users
> than are any bad decisions about programming languages or about how
> and where to implement some new feature.
> OK, I've violated my own rule about keeping posts short...just shows how
> useful "rules" are for Amber developers.... :-)
> ...dac
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> AMBER-Developers mailing list

Professor Kenneth M. Merz, Jr.
University of Florida Research Foundation Professor
Edmund H. Prominski Professor of Chemistry
Department of Chemistry
Quantum Theory Project
2328 New Physics Building
PO Box 118435
University of Florida
Gainesville, Florida 32611-8435


Phone: 352-392-6973
FAX: 352-392-8722
Cell: 814-360-0376

"The fundamental laws necessary for the mathematical treatment of a large part of physics and the whole of chemistry are thus completely known, and the difficulty lies only in the fact that application of these laws leads to equations that are too complex to be solved."

PAM Dirac, 1929

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Received on Sat Nov 05 2011 - 09:30:02 PDT
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