[gmx-users] free energy decomposition

Sanku M msanku65 at yahoo.com
Wed Oct 13 20:58:57 CEST 2010

I am aware of that paper by Pettit and Rossky where the suggested method is to 
get the entropy first by taking temperature derivative and substract that from 
PMF to get the enthalpy contribution  . 
BUT, also if you look at the recent paper   by Berk Hess ,  J.Phys.chem B , 
2010;114:11093 , you will find that ( figure 4 in page 11096 of that article) , 
Berk calculates average potential energy first and then substract that from PMF 
to get the entropy.  This is only one instance. There is also some other papers 
where they have first got the average energy .

 In that case, My question was that in gromacs, is it synonymous to using 
g_energy to get the potential energy of each windows   and then substract that 
from PMF to get the entropic part? If so, does one need to unbias the energy ( 
because of presence of biasing potential ) ?  

Can you clarify and provide any other opinion ?

Also, I did not understand David's comments: why it will work for constraints 
but not for umbrella sampling ?


From: Chris Neale <chris.neale at utoronto.ca>
To: gmx-users at gromacs.org
Sent: Wed, October 13, 2010 1:30:31 PM
Subject: [gmx-users] free energy decomposition

Sanku,  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 --  Hi,  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.  Sanku  

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20101013/96baa15e/attachment.html>

More information about the gromacs.org_gmx-users mailing list