[AMBER] Energy Calculations in Amber

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

Hi,

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


minyuan.mail.ustc.edu.cn
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Received on Sun Mar 04 2018 - 06:30:03 PST
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