Re: [AMBER] NETCDF problem

From: David A Case <>
Date: Fri, 14 Jan 2022 11:38:28 -0500

On Fri, Jan 14, 2022, Björn Karlsson wrote:

>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?

As a sanity check, run a short simulation (say 100 steps) and set ntwr=10,
so it will try to write a restart file every ten steps. See if you get
an error.

It may be that something else is going wrong with your simulation, and that
the write_nc_restart() error is a side effect. Your "many nanoseconds"
comment makes me suspect that this is a GPU run: is that correct? It would
be good to know more about your input parameters and system. Is this using
just standard forcefields, or have you created residues just for this
system? (If the latter, what force field did you use?)

It might be worth trying reducing dt as a test, especially if you are using
dt=0.004 now. You could be running into integration errors, and things like
vlimit checks are disabled on GPUs.


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Received on Fri Jan 14 2022 - 09:00:03 PST
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