[gmx-users] free energy decomposition

Chris Neale chris.neale at utoronto.ca
Wed Oct 13 21:44:21 CEST 2010


decomposing free energies into enthalpic and entropic components is not 
my particular expertise, but I'm astounded to hear that enthalpy equals 
the average forcefield energy. I would have thought that, at the very 
least, pressure work would also need to be incorporated.

Honestly, I can't help you any more though since I simply don't know 
enough about it. Good luck.


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 ?


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