Hello. The simulation which ended with the error message "cudaMemcpy
GpuBuffer error in pmemd.cuda" has not failed with sander.MPI. I have
run the same simulation using the same ig = 10703. Shouldn't I expect
the simulation to fail also with sander.MPI at the same stage?
Thank you
Fabrício
2012/9/17 Fabrício Bracht <bracht.iq.ufrj.br>:
> The distance between the Zn and the O in the water molecule is
> consistent throughout the entire simulation. Though it is a bit closer
> than I would expect it to be, it stands around 1.8 A in average (the
> reference value in the frcmod file is 2.2 A).
>
> Fabrício
>
> 2012/9/17 M. L. Dodson <mldodson.comcast.net>:
>> This may be wildly off base, but is the water still at a distance from
>> the Zn consistent with the distance you found when you parameterized
>> the system? What I am getting at is: has the Zn-associated water diffused
>> away? What is the distance in the last restart file before the simulation
>> stopped compared to the parameterized distance?
>>
>> Bud Dodson
>>
>> On Sep 17, 2012, at 3:46 PM, Fabrício Bracht wrote:
>>
>>> Hello. I have already had long discussions regarding this system in
>>> specific (http://archive.ambermd.org/201208/0174.html). The last
>>> discussion ended with my email:
>>>> I have deleted the bonds between the hydrogen atoms for this
>>>> particular water molecule (bound to the zinc atom). Used the flexible
>>>> water model and now the angle parameter for this water molecule is in
>>>> use. The md simulation has worked and the problem seems to be solved.
>>>> Are there any extra advices or perhaps some reading material I could
>>>> use to better understand the difference between using the flexible
>>>> water model or not?
>>>> Thank you again
>>>> Best regards
>>>> Fabrício
>>> I have not found the link for this particular discussion yet. The
>>> system is composed of an enzime with a zinc atom in its catalytic
>>> site. I have successfully run several hundred ns for a very very
>>> sismilar system, in which bound to the zinc atom is a hydroxyl group.
>>> This system now has a water molecule bound to the zinc atom. In my
>>> last discussion I have found that the only way for me to continue
>>> using the angle force parameters for this particular water molecule
>>> (which were the parameters that the MTK++ procedure gave), was to turn
>>> the flexible water model on. Now, the system has no apparent
>>> structural problems (bad geometry or collapsing hydrogen atoms etc),
>>> and yet, I still get the following error when I try to run pmemd.cuda.
>>>
>>> cudaMemcpy GpuBuffer::Download failed unspecified launch failure
>>>
>>> The error does not stop, however, the simulation from being restarted
>>> from the point where it has ended. I am running right now the same
>>> simulation under sander.MPI. But the system is quite large and I do
>>> not expect the results are in until the end of this week. By changing
>>> the seed I can, sometimes, run the entire simulation without any error
>>> messages. But then again, sometimes, it only takes a few steps for the
>>> simulation to stop. In previous discussions, I have discovered that
>>> the error is precision model independent (using either SPFP or SPDP or
>>> DPDP). The parameters for the similar system with the hydroxyl ion are
>>> very similar to this one, except for some specific bond constants
>>> (like the ZN-HOH bond and the H --- O bond) and, of course, the
>>> charge distribution. But other than that, the two systems are very
>>> alike.
>>> Any help here would be appreciated
>>> Fabrício
>>>
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>>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>> --
>> M. L. Dodson
>> Business email: activesitedynamics-at-gmail-dot-com
>> Personal email: mldodson-at-comcast-dot-net
>> Gmail: mlesterdodson-at-gmail-dot-com
>> Phone: eight_three_two-five_63-386_one
>>
>>
>>
>>
>>
>>
>>
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Received on Tue Sep 18 2012 - 11:00:05 PDT
