I am simulating a zinc containing protein using pmemd.cuda with a
GTX580 card. I performed a first thermalisation step using nmr
constraints to slowly increase the temperature (5 ns) up to 298 K.
After this I continued the simulation for about 3 ns using NVT scheme
in order to check stability problems. This simulation gave me a bit of
a headache, since the simulation often died out after a few hundred
steps or so (without any error warning in the log file). Once I gave
the input command for pmemd.cuda using nohup and the nohup.out file
gave a warning about kernel failure etc. I ran through the emails on
the list and found lots of stuff related to the card's temperature and
heating problems. I checked the temperatures and my card is not
overheating. I ran the simulation a few times to see if I could get a
consistent error (or failure) in order to report it here. Amazingly,
the last simulation I tried went all the way and completed without any
problem. After this, I started on an NPT step and now I get NaN values
in the log file after a few thousand steps. I had noticed that the NaN
values appeared right after a wrapping procedure, so I decided to
remove iwrap = 1 from the input file. The NaN values showed up anyway.
I parameterized the zinc active site using MTK++ manual instructions.
Any idea on what could be the problem?
Thank you
Fabrício Bracht
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Received on Mon Jun 18 2012 - 12:30:04 PDT
