[gmx-users] PMF and RDF

[sujithkakkat .]

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.

Regards,
Sujith.

On Tue, Dec 9, 2014 at 7:41 PM, Erik Marklund <erik.marklund at chem.ox.ac.uk>
wrote:

>
> On 9 Dec 2014, at 11:00, Erik Marklund <erik.marklund at chem.ox.ac.uk>
> wrote:
>
> > 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 pmts?
>
> To clarify what I meant, in light of what Justin wrote earlier, is that
> the pmf and ref can *in principle* be calculated from exactly the same
> data. The *conventional* way to get the pmf involves biasing the
> simulations to sample poorly populated regions, whereas the rdf is commonly
> inferred from simulations without such bias. In principle the rdf can also
> be obtained from biased simulations if that bias is corrected for during
> analysis, and similarly a pmf can be obtained without bias. As Justin said,
> there are many situations where the sampling is insufficient for some
> distances however.
>
> Erik
>
> >
>
> > Kind regards,
> > Erik
> >
> > 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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