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

From: Ross Walker <>
Date: Mon, 06 Jan 2014 12:59:10 -0800

The Monte Carlo barostat - both CPU and GPU.

On 1/6/14 9:41 AM, "Ross Walker" <> wrote:

>Ben Madej has been working extensively on this over the last few months so
>I will let him provide an update here but my understanding is that this is
>fixed although what is in the master branch is NOT up to date.
>NOTE to all - the GPU code (and quite a bit of the PMEMD code) in the
>master is VERY out of date and you should not be using this as your
>reference for how things stand. It was left like this because a lot of
>people use the git tree for production runs and I didn't want to cause
>issues with development code. The current state of the art for pmemd and
>pmemd.cuda is thus the GPU_Tachyon branch and this is where development
>has been going on. This week I plan to replace the master for
>$AMBERHOME/src/pmemd/ with the contents of GPU_Tachyon.
>All the best
>On 1/4/14 4:50 PM, "Jason Swails" <> wrote:
>>On Thu, Jan 2, 2014 at 10:20 AM, 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
>>> priority). There are reference implementations in mdgx and openMM;
>>> started a port to pmemd, but the code doesn't work. This would be a
>>> win
>>> both for efficiency and for physical realism.
>>Pawel seems to have found the problem, so this should be fixed before the
>>Amber meeting. We'll have to work with Scott in order to get the CUDA
>>taking maximum advantage of the performance benefits. The CUDA code will
>>work with the fixed barostat, but it still computes the virial which
>>negates one of the two advantages of the MC barostat in the first place
>>(the second, of course, being that the MC barostat is rigorously correct
>>from a stat mech viewpoint).
>>Cheers, and happy new year!
>>Jason M. Swails
>>Rutgers University
>>Postdoctoral Researcher
>>AMBER-Developers mailing list
>AMBER-Developers mailing list

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Received on Mon Jan 06 2014 - 13:00:05 PST
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