[AMBER] Energy Calculations in Amber

From: <minyuan.mail.ustc.edu.cn>
Date: Sun, 4 Mar 2018 22:10:54 +0800


After equilibration, systems are in stationary states.
To describe different system in terms of energy, which term in the mdout file should be used?
In amber advanced tutorial 21, I find that the binding enthalpy is calculated by H = <H>complex + <H>pure water - <H>host - <H>guest,
where each enthalpy H is the average values of the total potential energy for each system using awk command.

Similarly, to calculate reaction energy change, E = <E>product - <E>reactant, are the average energy values proper to use?

Looking forward to hear your help.

Best Wishes,
Yuan Min

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Received on Sun Mar 04 2018 - 06:30:03 PST
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