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