[gmx-users] free energy decomposition
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...
More information about the gromacs.org_gmx-users