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calculation of () Radial distribution function for the Lennard-Jones model fluid at =, =.. In statistical mechanics, the radial distribution function, (or pair correlation function) () in a system of particles (atoms, molecules, colloids, etc.), describes how density varies as a function of distance from a reference particle.
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 ...
Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) is a molecular dynamics program from Sandia National Laboratories. [1] LAMMPS makes use of Message Passing Interface (MPI) for parallel communication and is free and open-source software , distributed under the terms of the GNU General Public License .
Verlet integration (French pronunciation:) is a numerical method used to integrate Newton's equations of motion. [1] It is frequently used to calculate trajectories of particles in molecular dynamics simulations and computer graphics.
Figure 1 A 3on3 RDF Figure 2 Two-state trajectories. Description of RDF. A RDF is a lattice of substates, each substate represents either the on state or the off ...
Other applications are the virtual screening of ligands in drug discovery, in silico mutagenesis studies [2] [3] and antibody affinity maturation. [4] For the study of reactions it is often necessary to involve a quantum-mechanical (QM) representation of the reaction center because the molecular mechanics (MM) force fields used for FEP ...
The amplitude and phase of this scattered wave will be the vector sum of the scattered waves from all the atoms () = = [1] [2] For an assembly of atoms, f j {\displaystyle f_{j}} is the atomic form factor of the j {\displaystyle j} -th atom.
The Car–Parrinello method is a type of molecular dynamics, usually employing periodic boundary conditions, planewave basis sets, and density functional theory, proposed by Roberto Car and Michele Parrinello in 1985 while working at SISSA, [1] who were subsequently awarded the Dirac Medal by ICTP in 2009.