How did you define AAN, assuming it's non-standard? Can you share a
"saveoff ANN ann.lib" version?
Bill
On 2/23/17 8:05 PM, Alicia Merlino wrote:
> The odd thing is that I was able to succesfully run on cuda the same system
> but without the AAN ligand.
>
> 2017-02-24 0:12 GMT-03:00 Bill Ross <ross.cgl.ucsf.edu>:
>
>> Have you tried it on another GPU?
>>
>> Can you show the steps you took in leap to build your model? If they
>> might have included trying things manually at the leap cmd line, I would
>> put together a script and rebuild the prmtop 'clean', in case leap
>> propagated some bad state that only appears in cuda.
>>
>> Bill
>>
>>
>> On 2/23/17 6:23 PM, Alicia Merlino wrote:
>>> Hi, after the heating I succesfully switched back to 2 fs but I still
>> have
>>> troubles running with cuda. The same SHAKE error appears.
>>>
>>> 2017-02-23 2:01 GMT-03:00 Alicia Merlino <amerlino.fcien.edu.uy>:
>>>
>>>> I'll let you know!
>>>>
>>>>
>>>> 2017-02-23 1:38 GMT-03:00 Bill Ross <ross.cgl.ucsf.edu>:
>>>>
>>>>> It would be interesting to see if you could switch back to 2fs once
>>>>> things equilibrate.
>>>>>
>>>>> Bill
>>>>>
>>>>>
>>>>> On 2/22/17 8:32 PM, Alicia Merlino wrote:
>>>>>> That was with a time step of 1 fs if I change to 2 fs the calculation
>>>>>> crashes after 400 steps or so
>>>>>>
>>>>>> 2017-02-23 1:00 GMT-03:00 Alicia Merlino <amerlino.fcien.edu.uy>:
>>>>>>
>>>>>>> I've run the heating with pmemd for 5000 steps and it ended ok. I
>> don´t
>>>>>>> understand what's happening. I'll try a longer heating with ntpr=1 to
>>>>> see
>>>>>>> what happens.
>>>>>>>
>>>>>>> Thank you!
>>>>>>>
>>>>>>> 2017-02-23 0:30 GMT-03:00 Alicia Merlino <amerlino.fcien.edu.uy>:
>>>>>>>
>>>>>>>> Hi, with pmemd the simulation gets started and after 500 steps
>>>>> everything
>>>>>>>> seems to be ok.
>>>>>>>>
>>>>>>>>
>>>>>>>> 2017-02-22 23:26 GMT-03:00 David Case <david.case.rutgers.edu>:
>>>>>>>>
>>>>>>>>> On Wed, Feb 22, 2017, Alicia Merlino wrote:
>>>>>>>>>
>>>>>>>>>> Dear David, the calculation crashes while reading atomic
>> coordinates
>>>>>>>>> and
>>>>>>>>>> velocities with the error message that I reported before.
>>>>>>>>>>
>>>>>>>>>> Executable path: pmemd.cuda
>>>>>>>>> OK...now I see that you are running pmemd.cuda. Can you try a
>> short
>>>>>>>>> simulation using pmemd itself? Doesn't need to be very many steps:
>>>>> just
>>>>>>>>> set ntpr=1 so you can see if the simulation gets started OK.
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>>>>> 80: 177 - 178 and 81: 177 - 179
>>>>>>>>>>>>> Hydrogen atom 177 appears to have multiple bonds to atoms 178
>> and
>>>>>>>>> 179
>>>>>>>>>>>> which
>>>>>>>>>>>>> is illegal for SHAKEH.
>>>>>>>>>>>>> Exiting due to the presence of inconsistent SHAKEH hydrogen
>>>>>>>>> clusters.
>>>>>>>>> Amber developers: does anyone know if the atom numbers printed here
>>>>> (from
>>>>>>>>> gpu.cpp) start from zero or from 1?
>>>>>>>>>
>>>>>>>>> ....dac
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> _______________________________________________
>>>>>>>>> AMBER mailing list
>>>>>>>>> AMBER.ambermd.org
>>>>>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>>>>>>
>>>>>>>> --
>>>>>>>> Dra. Alicia Merlino
>>>>>>>> Profesora Adjunta del Laboratorio de Qca. Teórica y Computacional
>>>>>>>> Instituto de Química Biológica
>>>>>>>> Facultad de Ciencias, Universidad de la República
>>>>>>>> Iguá 4225, 11400 Montevideo, Uruguay
>>>>>>>> Tel: (+598) 2525 2186 <+598%202525%202186>
>>>>>>>> Fax: (+598) 2525 0749 <+598%202525%200749>
>>>>>>>>
>>>>>>> --
>>>>>>> Dra. Alicia Merlino
>>>>>>> Profesora Adjunta del Laboratorio de Qca. Teórica y Computacional
>>>>>>> Instituto de Química Biológica
>>>>>>> Facultad de Ciencias, Universidad de la República
>>>>>>> Iguá 4225, 11400 Montevideo, Uruguay
>>>>>>> Tel: (+598) 2525 2186 <+598%202525%202186>
>>>>>>> Fax: (+598) 2525 0749 <+598%202525%200749>
>>>>>>>
>>>>> _______________________________________________
>>>>> AMBER mailing list
>>>>> AMBER.ambermd.org
>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>>
>>>>
>>>> --
>>>> Dra. Alicia Merlino
>>>> Profesora Adjunta del Laboratorio de Qca. Teórica y Computacional
>>>> Instituto de Química Biológica
>>>> Facultad de Ciencias, Universidad de la República
>>>> Iguá 4225, 11400 Montevideo, Uruguay
>>>> Tel: (+598) 2525 2186 <+598%202525%202186>
>>>> Fax: (+598) 2525 0749 <+598%202525%200749>
>>>>
>>>
>>
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>>
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Received on Thu Feb 23 2017 - 20:30:03 PST
