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
Fax: (+598) 2525 0749
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Received on Wed Feb 22 2017 - 21:30:02 PST
