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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Received on Wed Jan 11 2012 - 19:30:03 PST
