POTENTIAL OF MEAN FORCE PDF DOWNLOAD

Potential of mean force. Where, the is the average force and therfore is the so-called Potential of Mean Force (PMF). A particular example would be that describes the interaction between two molecules held a fixed distance when the remaining molecules are canonically averaged over all configurations. See also this article (Wouter K. den Otter, "Revisiting the Exact Relation between Potential of Mean Force and Free-Energy Profile" J. Chem. Theory Comput. The potential of mean force (PMF) is defined as the the potential that gives an average force over all the configurations of a given system.


POTENTIAL OF MEAN FORCE PDF DOWNLOAD

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POTENTIAL OF MEAN FORCE PDF DOWNLOAD


Molecular Simulation/Potential of mean force

Abstract We apply concepts of covariant and contravariant vector space in differential geometry and general relativity to derive new, general, exact relations between potential of potential of mean force force and free-energy profile. These relations are immensely practical in free-energy simulations because a full Jacobian transformation which is usually unknown is not required; rather, only knowledge of the constraint coordinate of interest is needed.

POTENTIAL OF MEAN FORCE PDF DOWNLOAD

We reveal that in addition to the Jacobian determinant, the Jacobian scale factor and Leibnizian contributions must also be considered, as well a Fixman term with correct mass dependence. For a given separation between the two molecules, the Potential of mean force describes an average over all the conformations of the surrounding solvent molecules.

Various methods have potential of mean force proposed for calculating potentials of mean force. The simplest representation of the PMF is to use the separation between two particles as the reaction coordinate.

We also examine the sensitivity of the MD-PMF results to the choice of MD force field and compare PMFs for potassium, calcium and chloride ions to explore the basis for the valence selectivity of this narrow and uncharged ion channel.

Potential of mean force - Wikipedia

In a more practical way, the PMF can be used to know how the free energy changes as a function of a coordinate of the system. It can be a geometrical coordinate or a more general energetic solvent coordinate.

POTENTIAL OF MEAN FORCE PDF DOWNLOAD

Unlike the mutations used frequently in free energy perturbation calculations which are often along non-physical pathways, the PMF is usually calculated for a physical achievable process. In particular it is useful for predicting the rates potential of mean force chemical solution and for elucidating the reaction mechanism of condensed phase reaction such as enzymatic processes.



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