[gmx-users] query on decomposing potential of mean force

Sanku M msanku65 at yahoo.com
Tue Oct 12 23:35:27 CEST 2010


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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