[AMBER] NETCDF problem

From: Björn Karlsson <bjorn.karlsson.lnu.se>
Date: Fri, 14 Jan 2022 09:28:00 +0000

Dear all,
I’m currently running all-atomistic MD simulations of amyloid fibril in explicit (TIP3P) water and ion environment using pmemd.CUDA (iwrap=0, ioutfm=1 and ntxo=2) on one V100 card.
So far I’ve managed to collect 500ns of trajectory data and everything has until this point work out well. When I’m now trying to continue my simulations to collect more data my simulation stops with the message:

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.

With kind regards, Björn

Björn CG Karlsson
Associate Professor / Docent of Physical Chemistry

Physical Pharmacy Laboratory (PPL) – http://lnu.se/en/ppl

Linnæus University
Faculty of Health and Life Sciences
Department of Chemistry and Biomedical Sciences
391 82 Kalmar, Sweden
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Received on Fri Jan 14 2022 - 01:30:03 PST
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