From: Shivansh Seth (shivansh.seth_at_research.iiit.ac.in)
Date: Wed Apr 14 2021 - 23:01:16 CDT
I have been trying to run a simulation with 80 ABFs on different colvars (side chain dihedrals). The 7ns simulation ran without any errors but the final *.pmf, *.count, *.grad files were empty (0 bytes). All other files (colvar.state, restart, dcd) were non-empty and the simulation can be restarted without any errors. I tried reducing the number of ABFs (and colvars) to 20 and the final files were non-empty in this case. However, on the fourth restart, the files are again empty.
I'm using the CUDA accelerated version of NAMD 2.13 with 2 GeForce RTX 2080 Ti and 20 CPU cores. The run command is as follows:
namd2 +p20 +idlepoll +devices $CUDA_VISIBLE_DEVICES d1-4.conf > d1-4.log
One possible workaround we found was to use just 1 thread but that slows down the simulation significantly.
I have been stuck on this for a while now and any help would be much appreciated.
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