Re: [AMBER-Developers] Some notes and questions from the recent developers' meeting

From: Jason Swails <>
Date: Fri, 20 Feb 2015 17:57:15 -0500

> On Feb 20, 2015, at 5:23 PM, Ross Walker <> wrote:
> I believe the 'thing' people pay for should still be called AMBER - Lots of companies have approval for purchasing AMBER - if we suddenly change the name of what they are buying it will generate paperwork etc.
> So I think we should just simply have a free component of AMBER and a premium component. Simple solution would be to get rid of this weird AmberTools Fork - which I never liked in the first place since it just complicated build procedures, meant for a while we had multiple manuals and had to explain things in the tutorials etc and instead just finally merge everything back under AMBER - call it AMBER 15, roll in all the updates so far to pmemd and make the current git tree version of pmemd the AMBER 15 pmemd - move all the AmberTools out of it's own folder and back into the main source folder and then just have it be a standalone thing - consisting of two tar balls - Amber15.tar.bz2 and Amber15Pro.tar.bz2 or something like that (maybe have that include the Amber15 tar ball so we don't have this confusing thing of having to download two different things)

I would be on board with the naming convention. But I’m a strong -1 on moving everything into $AMBERHOME/src.

This is a *massive* change, and would probably rain down merge conflicts galore on anybody either (a) maintaining their own development branch or (b) that hasn’t pushed their changes to the git repo in several commits.

Not to mention the retooling it would require of update_amber, which would somehow have to get tested in advance of the release (and it is *not* easy to test a new system like that).

Moving sander was hard enough, and I think there are more places where paths are hard-coded than you realize, and I think you’re underestimating the challenge this will pose.

I also don’t think pmemd-master is ready to become the next pmemd release. There’s a lot of pmemd.amoeba-related work and new stuff in pmemd (MC barostat move sets and SGLD on the GPUs) that aren’t ready for release yet.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER-Developers mailing list
Received on Fri Feb 20 2015 - 15:00:02 PST
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