[gmx-users] PMF and RDF

Justin Lemkul jalemkul at vt.edu
Tue Dec 9 13:55:32 CET 2014

On 12/9/14 1:39 AM, sujithkakkat . 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.

For some systems, this may work, but only if the barriers are small enough that 
they can be sampled during normal MD.  For instance, we recently compared PMFs 
from umbrella sampling and from RDF for ions in water.  Given that the waters 
rarely displace from the ions' solvation shells (11 kcal/mol barrier in one 
case, for instance), there is a region with complete absence of sampling.  So, 
in some cases it may work, and in others (likely many) it will fail for 
practical reasons.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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