On 8/11/12 7:49 PM, Acoot Brett wrote:
Dear Justine,
For aideal protein system (no local minima in the MD), regardless of what the
seed number is, the system will converge to a same conformation, rihgt?
Not really - a single structure tells you nothing. Individual simulations
should sample conformational ensembles that are representative of their true
behavior. Only if you have evidence that individual simulations produce
reasonably similar *distributions* of structures do you have reason to claim
convergence. Again, there is a lot that you have to show to prove you've converged.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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