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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>>> 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>
>
--
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 Wed Feb 22 2017 - 21:00:02 PST
