I´ve tried it on 3 different GPUs with the same result
2017-02-24 1:05 GMT-03:00 Alicia Merlino <amerlino.fcien.edu.uy>:
> 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
>> >>>>>>>
>> >>>>>>>
>> >>>>>>> _______________________________________________
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>> >>>>>>> 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> <+598%202525%202186>
>> >>>>> Fax: (+598) 2525 0749 <+598%202525%200749> <+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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>> 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
Fax: (+598) 2525 0749
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Received on Thu Feb 23 2017 - 20:30:03 PST
