[gmx-users] free energy decomposition

Chris Neale chris.neale at utoronto.ca
Wed Oct 13 20:30:31 CEST 2010


This is not possible using g_energy or any other gromacs tool that I am aware of.
You must calculate the temperature derivative of the free energy.
See, for example, equation 16 in Pettitt BM, Rossky PJ. J Chem Phys. 1986;84:5836

-- original message --


I am studying Potential of mean force(PMF) of association of two peptides.  I
want to decompose the  PMF into energy(enthalpy) and entropic terms. But, I have
some queries on how to extract those contributions .

  I found, in  literature, generally, people try to get the energy(enthalpy)
first and then subtract it from PMF to get the entropic contribution. My
question is related to how to get the energy term first:

1. Will it be appropriate to just use g_energy tool on ener.edr file for each
windows obtained from umbrella sampling  and select the 'potential energy'
functionality term to get the*average potential energy*  for each windows ?
I used energy groups = system  in the .mdp file for each windows of my umbrella
sampling simulations.

2. If it is so, now I wonder whether  g_energy will give that potental energy
*in presence of umbrella bias*  .  If it is true, do one need to first unbias the
energy some how ( like using a boltzman factor) ?  However, I do not how to do

if you provide  any ideas, that will be great .

Here is the details on what I have done to get the PMF .

  I am studying Potential of mean force(PMF) of association of two peptides. For
this purpose , I have carried out GROMACS 4.0.7 umbrella sampling simulation by
dividing the reaction coordinate( i.e distance between center of mass of two
peptides) into around 25 windows of 0.1 nm separation.  Now, I have used WHAM
and got the PMF by unbiasing the umbrella potential.


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