Sir,
I have homology modeled protein (240 residues). I want to run
MD simulation in explicit solvent(TIP3P)with DIELECTRIC=1, constant
pressure. actually i am little bit confused about parameters, what
parameters should be used during the time of equilibration as well as
production, i also gone through the amber tutorial, At the
minimization time how i can know that protein has reached to its
convergence .
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Received on Fri Mar 05 2010 - 01:00:02 PST
