On 20/09/2012 7:26 PM, Wu Chaofu wrote:
Dear gmxers,
I have generated MD simulation trajectory using gmx, and now I want to
recalculate the energies and forces for the older trajectory by
excluding interactions between two defined groups. Therefore, the
older trajectory is used as one input option for mdrun through -rerun.
In my opinions, the newer run shoud much quicker than the older one
since only saved frames and less interactions are employed in this
calculation. However, I find that the speed is almost same. How to
decreasing CPU time for mdrun -rerun? I think I must have missed
something. Could you please give me some hints? Thank you a lot for
mdrun -rerun requires neighbour searching for every frame of the
trajectory, because it cannot assume spatial locality in the way that
mdrun can. So it is possible for a rerun to do more work than the
original. However in the absence of the timing breakdown reported at the
end of the .log files, there's nothing much else to be said.
Mark
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