AMBER Archive (2008)

Subject: AMBER: potential of mean force: Unit of PMF energies and min path

From: Catein Catherine (askamber23_at_hotmail.com)
Date: Thu Mar 20 2008 - 00:26:43 CDT

Dear Sir/Madam,
 
I am a new to PMF. I run the PMF calculations, and resolved the energy with WHAM. However, I have two questions:
 
(1) what is the unit of energy listed in the output WHAM? Is it kcal/mol?
 
(2) Can we find the minimum pathway in a 2D-PMF obtained by WHAM? If yes, could you mind to teach me how? Do I need to have write a script for doing this or can I do it with the amber package?
 
Best regards,
 
Cat
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