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

From: Ross Walker <>
Date: Mon, 06 Jan 2014 09:41:24 -0800

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master is VERY out of date and you should not be using this as your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 big
>> 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

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Received on Mon Jan 06 2014 - 10:00:03 PST
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