protein unfolding -- Phi MD

From: Wei Fu (
Date: Tue Nov 28 2006 - 13:59:29 CST

Dear NAMD users,

    I am trying to determine the transition state ensemble during protein
unfolding event by phi value
obtained from experiment by MD with NAMD. I guess that I need to
add an additional term obtained from the measured phi values to a standard
molecular mechanics potential function. I wonder if there is a script in
NAMD to do this? Or I just need to run a standard MD, then use phi value
to analyze trajectory? I am new to inverstigate protein unfolding event,
any idea will be highly appreciated!


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