I'm back on this now. There were some issues at work that needed attending
to that led to me missing this year's AMBER conference (yet again sigh)...
I'm not exactly sure this bug isn't fixed. But I'm about to look into it
again. How are you guys measuring RMSD?
On Wed, Jan 11, 2012 at 10:51 AM, Joshua Adelman <jla65.pitt.edu> wrote:
> 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 - 16:30:03 PST
