Re: [AMBER] AMBER error

From: David Case <>
Date: Thu, 25 May 2017 07:54:44 -0700

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.


AMBER mailing list
Received on Thu May 25 2017 - 08:00:03 PDT
Custom Search