thanks Bill for the quick reply the GPU in my system is GeForce GTX TITAN
(6GB).
*Atul Kumar Jaiswal*
Research Scholar
School of Computational and Integrative Sciences
Centre for Computational Biology and Bioinformatics (CCBB)
JNU, New Delhi
India.
On Wed, Apr 24, 2019 at 2:20 PM Bill Ross <ross.cgl.ucsf.edu> wrote:
> What GPU do you have? I know zilch, but I'd check the web pages for
> notes on it, if you haven't.
>
> Bill
>
> On 4/24/19 1:57 AM, wrote:
> > Dear amber users, I am trying to heat up a system at NVT to 50K by
> putting
> > a weak restrain on solute and the following is my input file:
> >
> > Heating: heating system at NVP upto 50K
> > &cntrl
> > imin = 0,
> > irest = 0,
> > ntx = 1,
> > ntb = 1,
> > cut = 10.0,
> > ntr = 1,
> > ntc = 2,
> > ntf = 2,
> > tempi = 0.0,
> > temp0 = 50.0,
> > ntt = 3,
> > gamma_ln = 1.0,
> > nstlim = 2500, dt = 0.002,
> > ntpr = 250, ntwx = 250, ntwr = 100
> > /
> > Keep DNA fixed with weak restraints
> > 60.0
> > RES 1 1487
> > END
> > END
> >
> > when I run the command
> > pmemd.cuda -O -i heat.in -o heat.out -p md.prmtop -c min1.rst -r
> heat1.rst
> > -x heat1.nc -ref min1.rst > heat1.log &
> >
> > the job is getting killed instantaneously with the following information
> in
> > the log file
> >
> > cudaMalloc GpuBuffer::Allocate failed out of memory
> >
> >
> > Please help me resolve this problem.
> >
> > thanks and regards
> > --
> > *Atul Kumar Jaiswal*
> > Research Scholar
> > School of Computational and Integrative Sciences
> > Centre for Computational Biology and Bioinformatics (CCBB)
> > JNU, New Delhi
> > India.
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>
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Received on Wed Apr 24 2019 - 02:00:03 PDT
