Re: [AMBER-Developers] New Year fixes for Amber

From: Josh Berryman <>
Date: Thu, 2 Jan 2014 16:46:06 +0100

>>4. We also need to update the *content* of the tutorials: removing
>>ones, bringing other up to date, and adding new ones

I've written a tutorial for free energy estimation with EMIL, comparing the
four basins on the Ramachandran plane of a dipeptide. It amounts to about
12 hours work in its current format, but could be cut down by providing
pre-equilibrated restart files.

Currently it is in latex/pdf but I have been planning to convert to html
and add to the tutorial collection once I have tested it on our MSc
students. They are scheduled to do the lab sometime in Feb.

While I am adding mine, I will have a look at other people's.

Where is the repo? Do I need to send public key to anyone?


On 2 January 2014 16:20, case <> wrote:

> Hi everyone, and happy new year!
> Below are some Amber updates that would be great to have some attention
> paid to, somewhat in order of decreasing priority. For the top few, it
> would
> be really great to have fixes available for Amber14.
> 1. Monte-Carlo barostat for pmemd and pmemd.cuda (and sander, with lower
> priority). There are reference implementations in mdgx and openMM; Jason
> started a port to pmemd, but the code doesn't work. This would be a big
> win
> both for efficiency and for physical realism.
> 2. Self-guided Langevin dynamics for pmemd and pmemd.cuda. There is a
> reference implementation in sander, and only a few lines of code (I think!)
> are involved. This is a win for cases where you don't know a good progress
> variable, and where torsional barriers (adjusted in aMD) are not
> necessarily
> the bottlenecks.
> 3. I'm looking for some eager soul to take a look at some of the Amber
> web pages. Just a basic knowledge of html is needed, so this would be
> appropriate for a high school or undergrad student. For starters, the
> awful syntax in the tutorials/index.htm file should be cleaned up...this
> page does not display properly in Chrome. It consists of tables within
> tables in a way that is really hard to follow. Cleaning it up, keeping
> the same content, would be a great start.
> I mentioned this on the developers' list a few months ago, but (aside from
> a
> flame war about wikis) there was no progress. The web site would be a
> great
> place for someone fairly new to Amber to pitch in, gain some visibility in
> the
> community, and provide a fresh eye to make things better.
> 4. We also need to update the *content* of the tutorials: removing
> out-dated
> ones, bringing other up to date, and adding new ones. At Rutgers, we're
> running an Amber workshop next week, and will try to post a second "basic"
> Amber tutorial focussed on green fluorescent protein: showing how to make
> the
> chromophore, run dynamics and output results. Dan has promised a tutorial
> on
> cpptraj. But there are other projects out there (arising, as I understand
> it,
> from other Amber workshops.) This would be a good time to spruce these up
> for
> general use.
> 5. Modest parallelization of mdgx, say using openmp and fftw3 capabilities
> for
> parallel 3D-FFT. This would be a win for connections to phenix, and for
> upgrading a bit the capabilities of the periodic code in AmberTools.
> Others might want to add to this list. I look forward to seeing some of
> you
> in Stony Brook soon.
> ....dac
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Received on Thu Jan 02 2014 - 08:00:02 PST
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