From: Jorgen Simonsen (jorgen589_at_gmail.com)
Date: Sun Jan 17 2010 - 20:42:30 CST
I have performed a ABF run sampling the dG of a torsion angle in a protein.
After 50 ns there is no longer a change in the dG which I have read is one
of the criteria for convergence but could I include another measure such as
average of force for the last 10 ns of the simulation which would be around
zero with some standard deviation?
When I started my simulation a choose a torsion angle which seemed
reasonable for me as a reaction coordinate but is there a better way to
justify the choice of reaction coordinate - I have read that it should be
the slowest vibrating how do I account for this?
Thanks in advance
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