AMBER: TI tutorial in Amber 8

From: huhu <lion_hjp.yahoo.com.cn>
Date: Wed, 8 Jun 2005 17:52:24 +0800 (CST)

 
Hi, Amber 8 user:

I am a new Amber8 user. When I re-do the TI example Thermodynamic integration calculations using sander listed in Amber web. I cant understand how to estimate free energy value by trapezoid method.

As far as I am concerned, I imagine that when clambda equal to 1, sampling must be done by MD, But it isnt computed in the tutorial. Here is what I understand in the method of estimating free energy value (trapezoid method). For example, clambda = 0, dv/dl = 5; clambda = 0.3, dv/dl = 4; clambda = 0.8, dv/dl = 6; clambda = 1, dv/dl =2; I would use the formula : Total(dv/dl)=[(5+4)*0.3+(4+6)*0.5+(6+2)*0.2]/2; I know my formula is wrong, but I dont understand the exact method to estimate the integral by hand. Please give me some suggestions for this question .

thank you in advance

huhu




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Received on Wed Jun 08 2005 - 12:53:00 PDT
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