I believe the literature tends to credit John Kirkwood with coining the
term "potential of mean force" (PMF). I think in this paper?
Kirkwood, J. G. J. Chem. Phys. 1935, 3, 300-313.
It was originally used to describe the behavior of (monoatomic?) fluids,
but has since been extended to describe arbitrary degrees of freedom,
usually progress coordinates for reactions (like atom transfer) or
conformational changes (like torsions). The term PMF is thus commonly used
(although maybe somewhat imprecisely) to refer to averaging over any number
and any kind of degrees of freedom beyond those of interest.
I could go on for a while, but I'll stop there,
Brian
On Tue, Nov 15, 2011 at 6:43 AM, Jan-Philip Gehrcke <jgehrcke.googlemail.com
> wrote:
> Thanks, Ross and Vitaly. I think I'll try to use the "potential" term
> whenever possible.
>
> While we're on it: how did the term "potential of mean force" emerge?
> When do we typically use it? The name suggests that certain interactions
> are incorporated only in average -- which ones?
>
> Cheers,
>
> Jan-Philip
>
> On 11/14/2011 08:24 PM, Ross Walker wrote:
> > Hi Jan,
> >
> > No I do not think it would he wrong to use FF99SB potential. I think the
> term force field is a historical one that probably derives from the fact
> that it is the derivative of the potential (i.e. The force) that is
> actually used in MD simulations rather than the potential.
> >
> > People typically write the AMBER equation in publications in terms of
> the energy but in reality what they are actually calculating in each time
> step is the force.
> >
> > All the best
> > Ross
> >
> >
> >
> > On Nov 14, 2011, at 11:15, Jan-Philip Gehrcke<jgehrcke.googlemail.com>
> wrote:
> >
> >> Hey,
> >>
> >> for the short time I am dealing with MD, I am wondering why the term
> >> "force field" was established and is so much more common than
> >> "potential". In my eyes, we are dealing with parameters for potential
> >> functions. Would it be weird or even wrong to use the term "Amber 99 SB
> >> potential" in a publication?
> >>
> >> Thanks for clarification,
> >>
> >> Jan-Philip
> >>
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> >
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>
>
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>
--
================================ Current Address =======================
Brian Radak : BioMaPS
Institute for Quantitative Biology
PhD candidate - York Research Group : Rutgers, The State
University of New Jersey
University of Minnesota - Twin Cities : Wright-Rieman Hall 101
Graduate Program in Chemical Physics : 610 Taylor Road,
Department of Chemistry : Piscataway, NJ
08854-8066
radak004.umn.edu :
radakb.biomaps.rutgers.edu
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Received on Tue Nov 15 2011 - 06:30:03 PST
