What is your command-line syntax? (i.e., how did you run pmemd.cuda?)
On Tue, May 8, 2012 at 10:27 AM, Marc van der Kamp <marcvanderkamp.gmail.com
> wrote:
> Hi,
>
> Well, the error message points to a probable cause; it says:
>
> Unit 16 Error on OPEN: md.rst
>
> So it appears that pmemd.cuda can't open the md.rst file for writing, and
> the job crashes when writing md.rst is attempted for the first time
> (ntwr=100000, so after 100000 steps). Is this correct? If so, you should
> probably check the write permissions etc.
>
> If you want to test this efficiently, use something like
> nstlim=10, ntpr=1, ntwr=2
> in your input.
>
> --Mar
>
> On 8 May 2012 15:16, Albert <mailmd2011.gmail.com> wrote:
>
> > hello:
> > I am using the following md.in for MD simulations with PMEMD.CUDA but
> > it terminate
> >
> >
> > production dynamics
> > &cntrl
> > imin=0, irest=1, ntx=5,
> > nstlim=20000000, dt=0.002,
> > ntc=2, ntf=2,
> > cut=10.0, ntb=2, ntp=1, taup=2.0,
> > ntpr=2000, ntwx=2000, ntwr=100000,
> > ntt=3, gamma_ln=2.0,
> > temp0=300.0,
> > /
> >
> >
> >
> > I tried many times, it always terminate after a few minutes of running.
> > I am wondering, what happen? is there anything wrong with my md.in file?
> >
> > thank you very much.
> >
> > Albert
> >
> >
> >
> >
> ----------------------------md.out--------------------------------------------------
> >
> >
> > NSTEP = 196000 TIME(PS) = 1692.000 TEMP(K) = 301.37 PRESS
> > = 190.5
> > Etot = -93344.7044 EKtot = 22508.2617 EPtot =
> > -115852.9661
> > BOND = 905.2599 ANGLE = 2415.4628 DIHED =
> > 3347.2978
> > 1-4 NB = 1092.6237 1-4 EEL = 11987.6085 VDWAALS =
> > 12588.5567
> > EELEC = -148189.7755 EHBOND = 0.0000 RESTRAINT
> > = 0.0000
> > EKCMT = 9541.3962 VIRIAL = 8051.4272 VOLUME =
> > 362241.7256
> > Density
> > = 1.0342
> >
> >
> ------------------------------------------------------------------------------
> >
> >
> > NSTEP = 198000 TIME(PS) = 1696.000 TEMP(K) = 297.58 PRESS
> > = -166.2
> > Etot = -93770.8213 EKtot = 22225.8613 EPtot =
> > -115996.6826
> > BOND = 847.2596 ANGLE = 2482.9980 DIHED =
> > 3334.3182
> > 1-4 NB = 1069.4747 1-4 EEL = 11918.1088 VDWAALS =
> > 12286.2835
> > EELEC = -147935.1254 EHBOND = 0.0000 RESTRAINT
> > = 0.0000
> > EKCMT = 9447.8886 VIRIAL = 10748.3041 VOLUME =
> > 362310.2508
> > Density
> > = 1.0340
> >
> >
> ------------------------------------------------------------------------------
> > Unit 16 Error on OPEN: md.rst
> >
> >
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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Tue May 08 2012 - 08:00:02 PDT
