AMBER Archive (2007)

Subject: AMBER:How to calculate the free energy of a series of conformations

From: huzehan19870731_at_126.com
Date: Mon Nov 19 2007 - 21:18:41 CST

Dear Amber users:
 
I'm a new AMBER user, and I am trying to calculating the free energy of each conformation in a trajactory simulated by conventional MD.
I know sander can do simple thermodynamic free energy calculation, or can computer potentials of mean force using umbrella sampling. My question is which method is better to attain my intention, and how to actualize the calculation.
Detailed input file and command will be very helpful.
 
Many thanks
 
Zehan Hu
 
 
 
 
 
 
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