[gmx-users] forceconstant of SMD
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!
Center for Drug Discovery & Design
State Key Laboratory of Drug Research
Shanghai Institute of Materia Medica
Chinese Academy of Sciences
294, Taiyuan Road
People's Republic of China
E-mail: yxu at mail.shcnc.ac.cn
& yxu at iris3.simm.ac.cn
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