From: Peiquan Chen (namd_at_eyou.com)
Date: Thu Nov 09 2006 - 02:26:46 CST
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.
dihe pmf (MAIN,1,C16) (MAIN,1,N18) (MAIN,1,C20) (MAIN,1,N21) barr=20, low=-180.0, high=180.0
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!
---- 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 pqchen_at_mail.nankai.edu.cn +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
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