Hello.
I have submit the same calculation using the same ig = 10703 twice
with pmemd.cuda in order to see if I could reproduce the error. The
simulation stopped at the exact same time. I used the restrt file of
this run to submit a new calculation using sander (serial) and got the
following error message:
vlimit exceeded for step 2; vmax = 26.1201
Coordinate resetting (SHAKE) cannot be accomplished,
deviation is too large
NITER, NIT, LL, I and J are : 0 3 2691 5317 5318
Note: This is usually a symptom of some deeper
problem with the energetics of the system.
I guess thet 5317 and 5318 are the atoms involved. These atoms are
part of the water molecule that is bound to the zinc atom. Could this
"symptom of some deeper problem with the energetics of the system"
mean that the parameters for the active site are not ok?
Thank you
Fabrício
2012/9/18 Fabrício Bracht <bracht.iq.ufrj.br>:
> 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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>>>
>>> --
>>> 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 Thu Sep 20 2012 - 09:00:02 PDT
