Re: [AMBER] problems with heating

From: Alicia Merlino <amerlino.fcien.edu.uy>
Date: Fri, 24 Feb 2017 01:52:53 -0300

2017-02-24 1:18 GMT-03:00 Bill Ross <ross.cgl.ucsf.edu>:

> How did you define AAN, assuming it's non-standard? Can you share a
> "saveoff ANN ann.lib" version?
>
> Bill
>
>
> On 2/23/17 8:05 PM, Alicia Merlino wrote:
> > 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>
> >>>>
> >>>
> >>
> >> _______________________________________________
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> >>
> >
> >
> >
> >
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>
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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 Thu Feb 23 2017 - 21:00:03 PST
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