Yes, it writes mdout.
I am running simulations for all 4 cases in different directories.
The pmemd job submission script works on a different machine without error.
Therefore, I believe this might have something to do with the way our local
HPC might had been setup.
On 26 May 2017 at 00:54, David Case <david.case.rutgers.edu> wrote:
> On Thu, May 25, 2017, Neha Gandhi wrote:
>
> > NetCDF error: Permission denied
> > write_nc_restart(): Could not open restart
> >
> > I have total 4 simulations with different peptide and I use similar input
> > files for the job using pmemd.cuda. 3 out of 4 simulations crashes with
> > above error whereas simulation 1 is still ongoing. I tried running
> crashed
> > simulations on other machine with gpu node, they work fine.
>
> Look at your actual pmemd/sander command lines. Is it possible you are
> using the same restart name for different runs? That would explain your
> symptoms: the first job to try to write to that file succeeded, but the
> ones
> after that failed because (unless you use the -O option) the program will
> not let you overwrite existing files.
>
> Of course, it could be something else. But the command line here is as
> important as knowing the contents of the mdin file.
>
> ....dac
>
>
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--
Regards,
Dr. Neha S. Gandhi,
Vice Chancellor's Research Fellow,
Queensland University of Technology,
2 George Street, Brisbane, QLD 4000
Australia
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Received on Thu May 25 2017 - 17:30:02 PDT
