[gmx-users] PMF and RDF

Justin Lemkul jalemkul at vt.edu
Wed Dec 10 13:44:50 CET 2014

On 12/9/14 11:51 PM, sujithkakkat . wrote:
> Hi Erik and Justin,
>    Thanks for the response.
>    Erik, I was thinking that in the case of hydrophobic solutes, there is a
> higher chance of proper sampling of all points along the inter solute
> distance. I believe the water shell around the hydrophibic solvent can
> break easier than the that in the case of ions. In that case I hope
> standard simulations can give better solute-solute RDFs and PMF may be
> avoided. The article which I refered to studies hydrophobic solutes and
> they have done PMF calculations.

This may work, but again it assumes that the energy barriers are relatively low 
and that the force field is sufficiently balanced against solute-water 
interactions that these transitions happen in an unbiased manner.  There's 
probably no way to know a priori whether or not it will work, but it's quick to 
find out.  For what it's worth, PMFs between small molecules are very cheap to 
compute, unlike larger macromolecular complexes, so there's only minimal gain by 
doing things this way.



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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