

AMBER Archive (2005)Subject: AMBER: TI tutorial in Amber 8 From: huhu (lion_hjp_at_yahoo.com.cn)Date: Wed Jun 08 2005  04:52:24 CDT
I am a new Amber8 user. When I redo 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
__________________________________________________
 
