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

From: Wu, Xiongwu (NIH/NHLBI) [E] <"Wu,>
Date: Fri, 3 Jan 2014 16:52:04 +0000

Hi Dave,

Happy New Year!
I will implement SGLD to pmemd and pmemd.cuda if no one else is doing it.
Thanks and see you at the Amber meeting.


> -----Original Message-----
> From: case []
> Sent: Thursday, January 02, 2014 10:20 AM
> To:
> Subject: [AMBER-Developers] New Year fixes for Amber
> 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 Fri Jan 03 2014 - 09:00:02 PST
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