Re: [AMBER-Developers] some thoughts about sander and Amber12

From: Yong Duan <>
Date: Wed, 30 Nov 2011 20:05:53 -0800

When Dave brought this up, I did not think much. Most of the exchanges
I've seen so far are more or less from technical perspective in terms
managing the package or facilitate the development.

I wonder what if we think from the administrative perspective. Again, I am
not in a position to even talk about this. But if I may, it might make
sense to think through the whole arrangement with UCSF and how does that
impact our ability to develop Amber or (more glorified sound bites: serve
the community).

About ten years ago, the "future" of Amber was discussed. There were
strong advocates for making Amber an open source. I was one of those who
opposed the idea. In retrospect, the decision of having our own package
was probably reasonable. But the cost seems also pretty high. Outside this
small community, Amber is viewed as a fee-supported. In reality, the fee
generated from the license supports such a small portion of the effort, it
probably did not make much difference. I think part of the problem has
been the license arrangement with UCSF. Ten years ago, it probably made
sense to have a person responsible for making and distributing CDs. Is it
still the case nowadays? While such service is valuable, I would think
that Amber can do as well without such a person, or perhaps even better if
we can devote the fund to support a couple of programmers who might work
on the user interface and expansion support or simply make it run faster.
We can then think strategically how to integrate Amber into the broad
modeling community. Right now, all these are just impossible. We can not
rely on an army of volunteers to run a for-fee package and expect to
compete with other well-funded efforts.

Oh, well, take this as a speech inspired by a bottle of merlot. :).

Yong Duan, Ph.D, Professor
UC Davis Genome Center and
Department of Biomedical Engineering
University of California at Davis
Davis, CA 95616
On 11/30/11 5:34 AM, "David A Case" <> wrote:
>I'm trying here to summarize the options for how sander fits into the next
>release of Amber.
AMBER-Developers mailing list
Received on Wed Nov 30 2011 - 20:30:03 PST
Custom Search