[gmx-users] free energy decomposition

David van der Spoel spoel at xray.bmc.uu.se
Wed Oct 13 20:42:41 CEST 2010

On 10/13/10 8:30 PM, Chris Neale wrote:
> 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
Recent versions of gromacs will actually plot the enthalpy in the energy 
file, and since your are only interested in the enthalpy difference that 
would work *if it wasn't for the umbrella sampling*. I think if you had 
used constraints rather than umbrellas this might do the trick.

Temperature dependence is of course a dependable way as well.

> -- 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

David van der Spoel, PhD, Professor of Biology
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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