On Tue, Sep 03, 2013, JAVAD MAHMOUDZADEH wrote:
> I am simulating a
> polymeric system with nearly 80000 atoms including water molecules in a
> truncated octahedron box. I am using GPU in the stage of production for
> calculations on amber 12 with a GTX680-4G card. I passed the minimization
> stages and heating using sander and a 50ps MD for density equilibration using
> pmemd.cuda with success. In the stage of production, using pmemd.cuda, unfortunately
> after around 29ns, the restart file became full of NaN and the density of the system
> became 0.02 and I observed *********** in front of EPtot and BOND in .out file.
Run a *much* shorter simulation, probably on a CPU. Watch the behavior of the
density. It might help to visualize the resulting trajectory. Try to use
mostly defaults in the input file (and/or post your mdin file). It seems
likely that your problem occurs way before 29 ns, but without more
information, people on the list cannot be of much help.
...dac
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Received on Tue Sep 03 2013 - 05:00:03 PDT
