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>
>> >>
>> >
>> >
>>
>>
>> _______________________________________________
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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 - 18:30:02 PST
