[AMBER] How to calculate the free energy change of a chemical reaction by the thermodynamic integration approach?

From: cwt <cwt_1986.163.com>
Date: Fri, 11 Oct 2013 14:18:00 +0800 (CST)

Dear all Amber users,

I am trying to calculate the reaction mechanism of an enzyme by the thermodynamic integration approach with Amber package. But I notice that in the thermodynamic integration, one should set the starting and ending states to calculate the energy difference between them. Previously I use umbrella sampling to get the potential mean force (PMF) of a reaction. I am confused if I want to use thermodynamic integration approach, should I define many groups along the reaction coordinate of reaction path, and add a constraint force on the atoms of reaction? Should I combine the thermodynamic integration with umbrella sampling?

Many thanks!

Wen-Ting Chu
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Received on Thu Oct 10 2013 - 23:30:03 PDT
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