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 can¡¯t 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 isn¡¯t 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 don¡¯t 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
