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
+46 772 28 80 00 Telephone exchange
+46 722 21 82 25 Mobile
bjorn.karlsson_AT_lnu.se
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Received on Fri Jan 14 2022 - 01:30:03 PST
