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

 
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

__________________________________________________
¸Ï¿ì×¢²áÑÅ»¢³¬´óÈÝÁ¿Ãâ·ÑÓÊÏä?
http://cn.mail.yahoo.com
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu