CCL: umbrella sampling using amber 8/9



Hi, everyone,
 
I am trying to analyze the reaction coordinate using umbrella sampling. What I want to do is to get the free energy along the reaction coordiate for ammonia transfer in a protein. This method is not very well documented in Amber's manual. Is there any similar example available? Or any advice. Thanks in advance.
 
Sincerely,
 
Yubo
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Dr. Yubo Fan               Email: yubofan,+,mail.chem.tamu.edu
Department of Chemistry    Tel:   1-979-845-5237
Texas A&M University
College Station, TX 77843
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