[gmx-users] free energy of system

Justin Lemkul jalemkul at vt.edu
Thu Apr 25 19:34:52 CEST 2013

On 4/25/13 12:02 PM, sarah k wrote:
> Dear all,
> I'm interested in calculating the Gibbs free energy of some systems. I
> have several questions in this regard:
> 1- The g_energy command gives some values in kJ/mol for total energy
> and enthalpy. Does the reported total energy include entropy effects?

Not likely.

> (The calculated total energy and enthalpy were not equal for the
> systems I had simulated.) Is the unit really kJ/mol?

Total energy and enthalpy should not necessarily be equal.  Total energy is just 
the sum of potential and kinetic energy.  The unit of kJ/mol is actually kJ per 
mole of equivalent systems.

> 2- Is it possible to perform md simulation as usual (like in the
> drug-enzyme tutorial) and run the g_bar command to get the dG results?

That depends on your definition of "as usual" and what you expect as a result. 
You can decouple a ligand from a binding site, but that only gives you part of 
the information you need to calculate, for instance, the actual free energy of 

> 3- How can I get the md_$LAMBDA.mdp file? Or which lines should be
> added to the common md.mdp files?

Given the nomenclature, I assume you are referring to files in my free energy 
tutorial, which are created by scripts.  All the answers to this question are in 
my tutorial.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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