Re: [AMBER] problems with heating

From: Alicia Merlino <amerlino.fcien.edu.uy>
Date: Fri, 24 Feb 2017 01:05:04 -0300

The odd thing is that I was able to succesfully run on cuda the same system
but without the AAN ligand.

2017-02-24 0:12 GMT-03:00 Bill Ross <ross.cgl.ucsf.edu>:

> Have you tried it on another GPU?
>
> Can you show the steps you took in leap to build your model? If they
> might have included trying things manually at the leap cmd line, I would
> put together a script and rebuild the prmtop 'clean', in case leap
> propagated some bad state that only appears in cuda.
>
> Bill
>
>
> On 2/23/17 6:23 PM, Alicia Merlino wrote:
> > Hi, after the heating I succesfully switched back to 2 fs but I still
> have
> > troubles running with cuda. The same SHAKE error appears.
> >
> > 2017-02-23 2:01 GMT-03:00 Alicia Merlino <amerlino.fcien.edu.uy>:
> >
> >> 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>
> >>>>>
> >>>>
> >>>
> >>> _______________________________________________
> >>> 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>
> >>
> >
> >
>
>
> _______________________________________________
> 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
Fax: (+598) 2525 0749



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Received on Thu Feb 23 2017 - 20:30:02 PST
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