Hi again,
Sorry to seem so impatient, but as Scot has fixed the problem with
pmemd.cuda for the combination of chamber prmtops and NPT, it would be
great to try this out / start using it soon.
Ross, is it possible to release the bugfix for this fairly soon?
Or else, would it be possible to send/post the required code change?
Many thanks,
Marc
On 12 January 2012 15:54, Marc van der Kamp <marcvanderkamp.gmail.com>wrote:
> 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
>> >>>
>> >>
>> >>
>> >
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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
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Received on Mon Jan 23 2012 - 06:30:03 PST
