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

From: Scott Brozell <>
Date: Sat, 5 Nov 2011 01:38:33 -0400


On Fri, Nov 04, 2011 at 11:28:03PM -0400, case wrote:
> 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.)
> 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

Ok, you have decided to keep the name AmberTools,
but what exactly does this mean vis-a-vis
unifying everything into a single src tree ?

> e. ...
> 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.

I agree. There is always room for improvement, but we are doing a good job:
I recently helped someone use neb in lammps; there is some documentation,
but no tutorial that i could find. The doc didn't define the acronyms
used in the program output, so one stumbling block was decoding the output,
EBF = Energy Barrier Forward, etc. I encounter a fair number of users
new to comp. chem., and these little things can be real roadblocks.

As far as Amber's neb tutorial, my main complaint is the tiny default
font for the section pages; yes, i know the key shortcut to make
it bIGGG, but then when i go back i get neon sign sized fonts.


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Received on Fri Nov 04 2011 - 23:00:04 PDT
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