[gmx-users] mdrun and simulation time

Francesco fracarb at myopera.com
Mon May 13 12:41:53 CEST 2013

Good morning all,
This morning I checked the output of a 8ns (4 x 2ns) of simulation and I
noticed a strange behaviour:
The fist two simulations (each 2ns) ended up correctly and they both
took 2h 06min to finish.
The second two were still running when the cluster time was over  (I
asked for 2.30)  and
were truncated.
My system contains around 160k atoms and all the previous 2ns simulation
took between 2h and 2h:10min (77 cores, no gpu).

I had a look at the log and it seems that in the last two simulations
did only 120.000 steps instead of 1.000.000.

Is it strange or it is possible/normal that with the increase of the ns
(always splitted in 2ns and extended) the running time is bigger?

thank you


Francesco Carbone
PhD student
Institute of Structural and Molecular Biology
UCL, London
fra.carbone.12 at ucl.ac.uk

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