[gmx-users] How many ps needs a simulation?

X.Periole X.Periole at rug.nl
Thu May 11 08:23:08 CEST 2006

On Wed, 10 May 2006 19:29:26 -0700 (PDT)
  jahanshah ashkani <ashkani_2003 at yahoo.com> wrote:
> Thanks,
>  In fact I have a sequence with 1277 residue. It is 
>stable even in 50ps. But when I continue to simulation my 
>pc is restarted in 40000 steps, automaticly. I should say 
>that this step needs about 100 h time.

50 ps for a protein of 1277 residue is probably equivalent
to the first minute of a marathon. The system size you
chose can be considered "enormous" !

Anyway as M and W already said, the simulation length that
would give you a reasonable answer depends entirely on 
question you want to answer and the quality of the answer
you want.

 From a 50ps simulation you have absolutely no answer at
all !!

Good luck

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