[gmx-users] free energy of system

[Justin Lemkul]

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 
binding.

> 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

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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