Antw: [gmx-users] free energy decomposition

Emanuel Peter Emanuel.Peter at
Thu Oct 14 09:08:18 CEST 2010


       I think the PMF is something like PMF = kT ln[g(r)] where g(r) is the radial distribution function from g_rdf.


>>> Sanku M  13.10.10 17.35 Uhr >>>
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 that. 

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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