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
Fax: (+598) 2525 0749
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Received on Wed Feb 22 2017 - 20:30:02 PST
