AMBER Archive (2003)

Subject: AMBER: PMF calculation

From: Lishan Yao (yaolisha_at_pilot.msu.edu)
Date: Thu Jul 24 2003 - 14:25:48 CDT

Hi there:
   I want to pull one ligand out of a protein. At first, I use Target MD
in amber7. It seems that it doesn't work well. For example, it is much
slower than a common MD simulation. And I couldn't use this method to do
simulation in solution. So now, I want to use PMF (potential of Mean
Force) method. Do you have any recommendation of good reference papers
about such kind of simulation done by using amber?

Best,
Lishan
  

-- 
Lishan Yao <yaolisha_at_pilot.msu.edu>
MSU

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