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
--
========================================
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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