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
Fax: (+598) 2525 0749
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Received on Wed Feb 22 2017 - 20:00:02 PST
