[AMBER-Developers] New Year fixes for Amber

From: case <case.biomaps.rutgers.edu>
Date: Thu, 2 Jan 2014 10:20:07 -0500

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.


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Received on Thu Jan 02 2014 - 07:30:02 PST
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