Thanks. Tried that as @MagnusL suggested above already which resulted in the same error reported 5 minutes ago.
My apologies, the previous test with changed barostat (c-rescale), tau_t (1) and tau_p (5) ended in the same error 719, not as I first reported (700, forgot to rerun grompp). I have revised the above message.
I tried extending both NVT and NPT from 100 ps to 10 ns. Both completed without issues. I next tried 100-ns MD (original md.mdp parameters), still got cuda error 719. I then reran an extended NPT to 100 ns (with your suggested modifications, i.e. c-rescale, tau_t=1,1; tau_p=5). The same cuda error occurred after 20 ns. So, it happens during equilibration and under positional restraints.
Thank you @hess @MagnusL for ideas. I think I’ll stop here for the time being. Issues remain unresolved.
What do you mean with equilibration and positional restraints?
Do both runs use position restraints? What ref-coord-scaling did you choose?
Both NVT and NPT were run with positional restraints of 1000,1000,1000 on all protein atoms. “refcoord_scaling = com” in NPT.
Could load upload a plot of the volume of the system over time?
That looks fully normal. Unfortunately I currently have no further ideas of how to find the cause of this.
Many thanks for looking into this and all the discussions. We’ll leave this for now.
This happened to me a couple of times when I was working on an HPC node, and several other MD simulation programs (amber (pmemd.cuda) and desmond) were running on the same node. Can this cause the problem?
