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The PMF can be obtained in Monte Carlo or molecular dynamics simulations to examine how a system's energy changes as a function of some specific reaction coordinate parameter. For example, it may examine how the system's energy changes as a function of the distance between two residues, or as a protein is pulled through a lipid bilayer.
This free-energy map is also known as a potential of mean force (PMF). Free-energy perturbation calculations only converge properly when the difference between the two states is small enough; therefore it is usually necessary to divide a perturbation into a series of smaller "windows", which are computed independently.
In probability theory and statistics, the moment-generating function of a real-valued random variable is an alternative specification of its probability distribution.Thus, it provides the basis of an alternative route to analytical results compared with working directly with probability density functions or cumulative distribution functions.
It is also possible to incorporate the effects of a solvent without needing any explicit solvent molecules present. One example of this approach is to use a potential mean force (PMF) which describes how the free energy changes as a particular coordinate is varied. The free energy change described by PMF contains the averaged effects of the ...
However, this use is not standard among probabilists and statisticians. In other sources, "probability distribution function" may be used when the probability distribution is defined as a function over general sets of values or it may refer to the cumulative distribution function, or it may be a probability mass function (PMF) rather than the ...
The pmf allows the computation of probabilities of events such as (>) = / + / + / = /, and all other probabilities in the distribution. Figure 4: The probability mass function of a discrete probability distribution. The probabilities of the singletons {1}, {3}, and {7} are respectively 0.2, 0.5, 0.3. A set not containing any of these points has ...
The graph of a probability mass function. All the values of this function must be non-negative and sum up to 1. In probability and statistics, a probability mass function (sometimes called probability function or frequency function [1]) is a function that gives the probability that a discrete random variable is exactly equal to some value. [2]
If X is a discrete random variable taking values x in the non-negative integers {0,1, ...}, then the probability generating function of X is defined as [1] = = = (),where is the probability mass function of .