Dear Gustavo,
Thanks for your kind reply.
I am already using ioufm = 1 (for binary trajectories )and iwrap = 1 .
And the **** in the energy values is also there, eg .
1-4 NB = ************** 1-4 EEL = ************** VDWAALS =
**************
And most importantly the same job is running well in cpu version of pmemd.
Can it be a bug with pmemd.cuda.MPI ?
On Wed, Apr 17, 2013 at 11:40 PM, Gustavo Seabra
<gustavo.seabra.gmail.com>wrote:
> Hi,
>
> what you are seeing in the restart file is likely *not* an error: the
> numbers are just too large for the output format. As you run longer
> calculations these days, this problem will just get more and more frequent.
> Its also likely that you will find some "***" in the mdcrd file as well.
>
> Some possible solutions are:
> 1. Use iwrap=1
> 2. Use binary (NetCDF) files.
>
> Please see the manual for the details.
>
> Cheers,
>
> Gustavo Seabra
> Professor Adjunto
> Departamento de Química Fundamental
> Universidade Federal de Pernambuco
> Fone: +55-81-2126-7450
>
>
> On Wed, Apr 17, 2013 at 3:03 PM, HIMANSHU JOSHI <himanshuphy87.gmail.com
> >wrote:
>
> > Dear friends,
> >
> > I am running pmemd.cuda.MPI for a system with approximately 1/2 million
> > atoms with dna and wate, After energy min and equilibration, I tried to
> do
> > production run with constant pressure (flag : ntb =2 ntp =1) but its
> > giving error *** in the restart file and energy values in output file
> after
> > running few steps (~ 30 ps). The same job with same input files is
> running
> > well in cpu version of pmemd (pmemd.mpi).
> >
> > Earlier the same system I ran with constant volume simulation (ntb = 1 )
> in
> > gpu with same pmemd.cuda.MPI and it ran well.
> >
> > So there is some problem with pmemd.cuda.MPI with npt simulation !!!
> >
> > Can anyone assure me.
> >
> > I have applied the latest bugfixes to amber 12 amber (Version 12.2) dated
> > (01/10/2013) for both cpu and gpu.
> >
> > Looking forward for some constructive comments from amber community .
> > Thanks for your kind attention.
> >
> >
> > --
> > *With Regards,
> > HIMANSHU JOSHI
> > Graduate Scholar, Center for Condense Matter Theory
> > Department of Physics IISc.,Bangalore India 560012*
> > ॐ सर्वे भवन्तु सुखिनः सर्वे सन्तु निरामयः।
> > सर्वे भद्रणिपश्यन्तु मा कश्चिद्दुःख भाग भवेत्॥
> > <
> >
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--
*With Regards,
HIMANSHU JOSHI
Graduate Scholar, Center for Condense Matter Theory
Department of Physics IISc.,Bangalore India 560012*
ॐ सर्वे भवन्तु सुखिनः सर्वे सन्तु निरामयः।
सर्वे भद्रणिपश्यन्तु मा कश्चिद्दुःख भाग भवेत्॥
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Received on Wed Apr 17 2013 - 11:30:03 PDT
