Hi Ross,
On Jan 11, 2012, at 1:42 PM, Ross Walker wrote:
> Hi Josh,
>
>> I would just add that I'm also very interested in seeing this bug
>> resolved soon as well, and it would be great to know approximate
>> timescales of when we might expect a patch. I'm not sure if having two
>> users vs one interested in this shifts any priorities around, but I
>> figured it couldn't hurt to suggest Marc isn't the only one interested
>> in running CHAMBER generated systems using pmemd.cuda.
>
> The patch for this was made but looks like it needs more testing. I was
> hoping to have that done by now but other things keep getting in the way.
> The current plan is to focus on making sure it works for AMBER 12 and then
> back porting a patch for AMBER 11.
>
> In the meantime the issue should only be affecting NPT calculations. You
> could run the CPU version of the code to equilibrate the density with NPT
> and then switch to NVT to use the CUDA code.
>
The only complication on our end with moving to NVT is that we're looking at conformational changes of a protein embedded in a membrane, which could result in the protein changing the volume it consumes in the bilayer. I would just be concerned that fixing the box dimensions could have unwanted consequences for either the protein or the lipids's behavior.
I guess I'll just have to patiently wait for the testing to play itself out. Again it would be helpful to have a rough idea of timescales (weeks or months) you think it could reasonably take to make the patch public.
Thanks again for your insight.
Josh
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Received on Wed Jan 11 2012 - 11:00:03 PST
