[gmx-users] forceconstant of SMD

Xu Yong yxu at mail.shcnc.ac.cn
Mon Dec 23 13:33:41 CET 2002

Hi, Dear all

I am now doing some SMD work. I don't understand the meaning of parameter in the pull.ppa
there are 'pullrate'   and 'forceconstant'.
the default forceconstant is 100 (kJ/mol nm). if I can modify it to other number?
I have use 100 and 500 in this option with same velocity but under the former condition, the small molecule is still almost the same position, and under the latter  condition, thesmall molecule is pulled 30A. 
would you please tell me that what number should I set for forceconstant? how to determine the proper velocity, 0.05A/ps or more slow?  when I use 500 as forceconstant and use different velocity, I obtained almost the same force plot.
what procudure should I take to do a convincingly SMD?

any answer would be very appreciated!

Best Regard 				

Xu Yong

 Center for Drug Discovery & Design     
 State Key Laboratory of Drug Research
 Shanghai Institute of Materia Medica
 Chinese Academy of Sciences
 294, Taiyuan Road
 Shanghai 200031
 People's Republic of China
 E-mail: yxu at mail.shcnc.ac.cn 
       & yxu at iris3.simm.ac.cn
 Phone: 86-21-64311833-615/222(L)
   Fax: 86-21-64318401

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