AMBER Archive (2008)

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

From: David A. Case (case_at_scripps.edu)
Date: Sun May 18 2008 - 15:09:00 CDT

On Tue, May 13, 2008, Catein Catherine wrote:
>
>
> 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?

This was a one-dimensional PMF, so we just use a simple Simpson's rule
numerical quadrature scheme. The integral is over exp(-beta*W) dq, where W is
the PMF. So the answer has units of length.

...hope this helps....dac

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