Excellent Scot, many thanks!
Ross, do you think this could be released as a (separate) bugfix for
AMBER11?
That would be great.
Thanks,
Marc
On 12 January 2012 15:47, Scott Le Grand <varelse2005.gmail.com> wrote:
> Fix checked in... Off to adding NH4+ SHAKE support now (in 3 years no one
> ever complained about this: Until now)...
>
> On Wed, Jan 11, 2012 at 7:03 PM, Scott Le Grand <varelse2005.gmail.com
> >wrote:
>
> > Found it...
> >
> > Checking in fix shortly:
> >
> > GPU DPDP:
> > NSTEP = 200 TIME(PS) = 200.400 TEMP(K) = 298.54 PRESS =
> > 236.8
> > Etot = -114607.6739 EKtot = 27373.9425 EPtot =
> > -141981.6164
> > BOND = 996.2311 ANGLE = 2512.1603 DIHED =
> > 1647.9070
> > UB = 323.5942 IMP = 159.1814 CMAP =
> > -380.4425
> > 1-4 NB = 922.7533 1-4 EEL = 10149.6941 VDWAALS =
> > 11075.4372
> > EELEC = -169388.1325 EHBOND = 0.0000 RESTRAINT =
> > 0.0000
> > EKCMT = 11764.1346 VIRIAL = 9529.6640 VOLUME =
> > 436985.4968
> > Density =
> > 1.0467
> >
> > CPU:
> > NSTEP = 200 TIME(PS) = 200.400 TEMP(K) = 298.53 PRESS =
> > 237.0
> > Etot = -114607.9710 EKtot = 27373.6615 EPtot =
> > -141981.6325
> > BOND = 996.2197 ANGLE = 2512.1427 DIHED =
> > 1647.8892
> > UB = 323.5874 IMP = 159.1712 CMAP =
> > -380.4489
> > 1-4 NB = 922.7679 1-4 EEL = 10149.7372 VDWAALS =
> > 11074.9732
> > EELEC = -169387.6720 EHBOND = 0.0000 RESTRAINT =
> > 0.0000
> > EKCMT = 11764.3560 VIRIAL = 9528.0691 VOLUME =
> > 436985.2915
> > Density =
> > 1.0467
> >
> >
> >
> >
> >
> >
> > On Wed, Jan 11, 2012 at 4:14 PM, Scott Le Grand <varelse2005.gmail.com
> >wrote:
> >
> >> 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
> >>> _______________________________________________
> >>> AMBER mailing list
> >>> AMBER.ambermd.org
> >>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>
> >>
> >>
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Jan 12 2012 - 08:00:04 PST
