On Thu, Jan 2, 2014 at 10:20 AM, case <case.biomaps.rutgers.edu> 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.
>
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 code
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
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Sat Jan 04 2014 - 17:00:03 PST
