Ok. Thank you very much
Best regards
Fabrício
2012/9/20 Ross Walker <ross.rosswalker.co.uk>:
> Hi Fabricio,
>
> The mailing list message limit is 1MB to prevent people sending massive
> emails that can clog up everyones in box. Your email with the attachments
> was held because it exceeded this. I have forwarded the held email to
> myself directly though so have a copy of the files. I'll try to take a
> look at it tomorrow.
>
> All the best
> Ross
>
>
> On 9/20/12 2:36 PM, "Fabrício Bracht" <bracht.iq.ufrj.br> wrote:
>
>>Hello Ross. I have sent an email to the amber mailing list with the
>>files attached. I do not know if you block emails with attached files
>>or not. Could you please confirm if the email arrived or not?
>>Thank you
>>Fabrício
>>
>>2012/9/20 Ross Walker <ross.rosswalker.co.uk>:
>>> Hi Fabricio
>>>
>>> Can you post your input files? I looked through the threads and couldn't
>>> find any. Without these it is a little difficult to help. I suspect the
>>> problem is some kind of illegal (or marginal) bonding or other subtle
>>> problem with the initial topology file. Sander tends to be much more
>>> tolerant of slightly dodgy topologies than the CUDA code, it also has
>>> little to no error checking of things that should not really be allowed,
>>> or are assumed should not occur, e.g. hydrogens with multiple bonds that
>>> are shaken, atoms bonded to themselves, etc.
>>>
>>> Did you take a look at the starting structure that gives the limit
>>>error -
>>> is there anything obviously wrong with it? - This is going to take
>>>quite a
>>> bit of debugging to figure out what is going on. I would start by trying
>>> to look very carefully at what is going wrong with the initial
>>>structure.
>>>
>>> Note, the GPU code is deterministic so if you use the same random see
>>>you
>>> will get identical (forever!!!) results which is what you see. You could
>>> try with different random seeds and see if it still blows up but I think
>>> the problem is much deeper routed than a simple instability. Also note
>>> that you will not be able to make sander match the GPU code - you can
>>> converge it to the same ensemble but not get it to give identical
>>> trajectories. You can make NVE match for a few thousand steps before
>>> roundoff error causes divergence but with anything that uses random
>>> numbers it will be impossible, even with the same random seed, since the
>>> actual random number generators used in sander and in pmemd.cuda are
>>> different. Hence the same random see will not unfortunately generate the
>>> same sequence of random numbers.
>>>
>>> Post your input files and I'll try to take a look.
>>>
>>> All the best
>>> Ross
>>>
>>>
>>> On 9/20/12 8:39 AM, "Fabrício Bracht" <bracht.iq.ufrj.br> wrote:
>>>
>>>>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
>>>>>>>>
>>>>>>>> _______________________________________________
>>>>>>>> AMBER mailing list
>>>>>>>> AMBER.ambermd.org
>>>>>>>> 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 Thu Sep 20 2012 - 15:30:03 PDT
