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Lemkul et al. have used steered molecular dynamics simulations to calculate the potential of mean force to assess the stability of Alzheimer's amyloid protofibrils. [6] Gosai et al. have also used umbrella sampling simulations to show that potential of mean force decreases between thrombin and its aptamer (a protein-ligand complex) under the ...
An alternative to free-energy perturbation for computing potentials of mean force in chemical space is thermodynamic integration. Another alternative, which is probably more efficient, is the Bennett acceptance ratio method. Adaptations to FEP exist which attempt to apportion free-energy changes to subsections of the chemical structure. [5]
It was later followed by the potential of mean force (statistical PMF [Note 1]), developed by Sippl. [3] Although the obtained scores are often considered as approximations of the free energy—thus referred to as pseudo-energies—this physical interpretation is incorrect.
There are various types of potential energy, each associated with a particular type of force. For example, the work of an elastic force is called elastic potential energy; work of the gravitational force is called gravitational potential energy; work of the Coulomb force is called electric potential energy; work of the nuclear force acting on the baryon charge is called nuclear potential ...
Force fields utilize the same concept as force fields in classical physics, with the main difference being that the force field parameters in chemistry describe the energy landscape on the atomistic level. From a force field, the acting forces on every particle are derived as a gradient of the potential energy with respect to the particle ...
The Lennard-Jones potential is a simple model that still manages to describe the essential features of interactions between simple atoms and molecules: Two interacting particles repel each other at very close distance, attract each other at moderate distance, and eventually stop interacting at infinite distance, as shown in the Figure.
A thermodynamic potential (or more accurately, a thermodynamic potential energy) [1] [2] is a scalar quantity used to represent the thermodynamic state of a system. Just as in mechanics , where potential energy is defined as capacity to do work, similarly different potentials have different meanings.
If the force is zero, then the potential is a constant (by definition). In a combination of the continuously distributed model which gave the Poisson–Boltzmann equation and the model of the point charge, it is assumed that at the radius a i {\displaystyle a_{i}} , there is a continuity of φ ( r ) {\displaystyle \varphi (r)} and its first ...