AMBER Archive (2007)

Subject: AMBER: Steered MD & Jarzynski's equality

From: James W (c00jsw00_at_nchc.org.tw)
Date: Wed May 02 2007 - 01:44:20 CDT

Dear all ,
#the reference : (http://en.wikipedia.org/wiki/Jarzynski_equality)
I confused the Jarzynski's equality . The equality is shown:
exp (-F/KT) = < exp (-W/KT) > .
&
F = < W > + ......
I used SMD module of CHARMM and obtained the reaction coordinates &
work ,like this :
______________________________________________________
57.00000 57.73576 -1471.51842 0.00000
57.00093 57.34648 -691.10171 -1.00562
(RC) (WORK)
*RC : reaction coordinates
I wanted to obtain the " < W > " form my data . My method is :
1. S = sum { exp (-W(i) /kT )} , i = 1 ....N
2. p(i)= exp (-W(i) /kT ) / S
3. <W(i)> = W(i)*p(i) / S

Could you tell me that my method is right ?

Wang 

--
National Center High-performance Computing (http://www.nchc.org.tw)

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