Dear AMBER users,
When we finish the MD simulation, we got a large number of mdcrd files.
In the old days, we check the rmsd change over time, when the rmsd become constant, we define the system is converged, and production period start where we can do the ptraj (hbond, average pdb, etc....).
Recent trends seems to be doing clustering analysis instead. We don't need to check the rmsd changes over time. Sometime, we just do multiple simulations with different starting structures.
Based on your experience, when we do the clustering analysis, do we still need to check if the system is converged? If yes, what is the right approach?
If we are doing the long simulation, should we still do the clustering analysis only for the production period? How about the equilibrium period? Should we also include those mdcrd files starting from time zero?
Best regards,
Catherine
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Received on Wed Oct 17 2012 - 10:30:03 PDT
