Question about free energy of conformation change

From: Peiquan Chen (
Date: Thu Nov 09 2006 - 02:26:46 CST

Hi all,

I am going to use the free energy of conformational changes module in NAMD to study the free energy profile roting of one bond of my inhibitor. But just as I am a newbie in this class of calculation, I have something uncertain and want to know.

In my configuration file, I have define as following.

freeEnergy on
freeEnergyConfig {

   urestraint {
   dihe pmf (MAIN,1,C16) (MAIN,1,N18) (MAIN,1,C20) (MAIN,1,N21) barr=20, low=-180.0, high=180.0

mcti {
  task = stepup
  equiltime = 50 ps
  accumtime = 250 ps
  numsteps = 36
  print = 1 ps

I have the following question:

1. I don't know which value for barr is suitable for my molecule. I just take 20 as described in the use guide.

2. Which values I should take in equiltime and accumtime?

3. How to judge I have done a succesful simulation if we don't have any experimental data about the conformation change.

Any commment will be appreciated!

Sincerely yours

PeiQuan Chen
PeiQuan Chen, Ph.D Student, Department of Chemistry, Nankai University
WeiJin Road 94, TianJin, 300071, P.R.China
phone:	(86)2223494034(HOME) (86)23504991(LAB) Mobile Phone: (+86)13920675030

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:42:48 CST