Re: [AMBER] NETCDF problem

From: Björn Karlsson <>
Date: Fri, 14 Jan 2022 13:27:46 +0000

Dear David,
Thanks for confirming my believes regarding the use of the NETCDF-files.
I've carefully checked my job-file and the -O flag is always present before each run.
Moreover, the simulation actually starts and runs for many nanoseconds before the error message pops up (how many nanoseconds vary from simulation to simulation basd on the use of ig=-1) so based on this I wouldn't be related to the use of the -O flag right?

With kind regards, Björn

On 2022-01-14, 14:16, "David A Case" <> wrote:

    On Fri, Jan 14, 2022, Björn Karlsson wrote:
>NetCDF error: Input/output error
>write_nc_restart(): Could not open restart
>As far as I can understand this message informs me that the restart file is
>corrupt due to coordinate overflow (this is also confirmed when I convert
>the binary restart-file to a pdb-file and then look at the coordinates for
>diffusing water molecules). My believe was however that the use of binary
>NETCDF-files would prevent this behavior. Can anyone please help me to
>clear out what is happening here.

    Your understanding of netcdf format is correct. However, the above message
    looks like it is happening when write_nc_restart is called, i.e. when you
    are trying to output a new netcdf restart file at the end of your new run.

    Check your file names carefully. Unless you set the "-O" flag, amber will
    not overwrite an existing file, which could lead to the above error if the
    requested restart file already exists. But it could be some other
    permissions problem as well.


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