AMBER Archive (2008)

Subject: AMBER: An enquiry about dynamic simulations of oxygen binding to myoglobin (Ann N Y Acad Sci. 1986;482:222-

From: Catein Catherine (askamber23_at_hotmail.com)
Date: Tue May 13 2008 - 05:17:29 CDT

Dear Sir/Madam,
 
For the dynamic simulations of oxygen binding to myoglobin (Ann N Y Acad Sci. 1986;482:222-33). I noted the rate constant was calculated by PMF approach.
 
Could you mind to let me know how to calculate the integral over the initial state of a PMF profile (eq.3)? Do you need a special software to integrate the values? Should we integrate the energy * coordinate or energy / coordinate?
 
Best regards and many thanks in advanced,
 
Cat
 
 
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