[gmx-users] PMF and RDF

Erik Marklund erik.marklund at chem.ox.ac.uk
Tue Dec 9 12:00:18 CET 2014

Dear Sujith,

Umbrella sampling does exactly that, but adds a biasing potential to sample high-energy regions of the reaction coordinate in separate simulations. The -px output when you do umbrella sampling with mdrun is indeed a sampling of distances along the reaction coordinate, which if you histogram it is the rdf. g_wham uses that data (or alternatively the force along the reaction coordinate instead of the distance) to build a PMF. My question to you is why do you think rdfs are significantly easier than pmfs?

Kind regards,

On 9 Dec 2014, at 06:39, sujithkakkat . <sujithks58 at gmail.com> wrote:

> Dear all,
>     I read in *Phys. Chem. Chem. Phys., 2009, 11, 10427-10437*, that the
> radial distribution function is directly related to Potential of mean force
> through RDF=exp(-PMF/kT).
>     My question is why would someone worry about computing PMF in a simple
> case like interaction between two small solute molecules in water , along
> the intermolecular distance, when one can get the RDF between the solutes ,
> which I believe is easier than PMF calculation.
>      Another article *Biophysical Chemistry 101-102 (2002), 295-307 *reports
> PMF between solute molecules from Monte Carlo simulations. Why not just
> find RDF.
> Regards,
> Sujith.
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