[gmx-users] How Long to Equlibrate?

Mark Zottola mzottola at gmail.com
Thu Jul 26 14:19:15 CEST 2007

I have a 290+ residue protein and I recently ran a 200 ps simulation in a
water box with electrostatic cutoff at approximately half the value of
the box dimension.  Since there is no heating stage in the dynamics, I am
wondering what guidelines there are for knowing when to evaluate data from
the simulation.  There are some interesting features to the RMSD plot I
would like to investigate. But I am not sure I can analyze the last 100 ps
of the dynamics or not.  Any help would be greatly appreciated.


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