Molecular Dynamics Simulations
Expert-defined terms from the Certificate in Quantum Espresso And VASP Theory course at HealthCareCourses (An LSIB brand). Free to read, free to share, paired with a professional course.
Aba Initio Calculations refer to a type of quantum mechanical calculation… #
Related terms include density functional theory and post Hartree-Fock methods. In Molecular Dynamics Simulations, Aba Initio Calculations are used to calculate the potential energy surface of a system, which is then used to simulate the dynamics of the system.
Ab Initio Molecular Dynamics is a type of molecular dynamics simulation that use… #
Related terms include Car-Parrinello molecular dynamics and quantum molecular dynamics. In this type of simulation, the electronic structure of the system is calculated using Aba Initio Calculations, and the forces on the atoms are calculated using the Hellmann-Feynman theorem.
Adiabatic Approximation is an approximation used in molecular dynamics si… #
Related terms include Born-Oppenheimer approximation and non adiabatic effects. In this approximation, the electronic structure of the system is calculated using quantum mechanical calculations, and the nuclear motion is treated classically.
Algorithm refers to a set of instructions used to solve a specific proble… #
Related terms include numerical methods and computational techniques. In Molecular Dynamics Simulations, algorithms are used to integrate the equations of motion, calculate the forces on the atoms, and update the positions and velocities of the atoms.
Anharmonic Effects refer to the deviations from the harmonic appro… #
Related terms include quantum effects and anharmonic corrections. In Molecular Dynamics Simulations, anharmonic effects can be important for systems with high temperatures or large amplitude motions.
Atomic Orbital refers to a mathematical function that describes the distr… #
Related terms include atomic basis sets and molecular orbitals. In Molecular Dynamics Simulations, atomic orbitals are used to calculate the electronic structure of a system.
Atomic Simulation Environment is a software package used to perform molec… #
Related terms include simulation software and computational tools. In this software package, users can define the system to be simulated, choose the simulation parameters, and analyze the results.
Band Structure refers to the relationship between the energy of an ele… #
Related terms include electronic structure and density of states. In Molecular Dynamics Simulations, the band structure of a system can be calculated using quantum mechanical calculations.
Basin Hopping is a global optimization algorithm used to find the glob… #
Related terms include optimization algorithms and global minimization. In Molecular Dynamics Simulations, basin hopping can be used to find the most stable structure of a system.
Basis Set refers to a set of mathematical functions used to describe the… #
Related terms include atomic orbitals and molecular orbitals. In Molecular Dynamics Simulations, basis sets are used to calculate the electronic structure of a system.
Boltzmann Distribution is a probability distribution used to describe the… #
Related terms include canonical ensemble and thermal fluctuations. In Molecular Dynamics Simulations, the Boltzmann distribution is used to sample the phase space of a system.
Born #
Oppenheimer Approximation is an approximation used in molecular dynamics simulations, where the electronic degrees of freedom are separated from the nuclear degrees of freedom. Related terms include adiabatic approximation and non adiabatic effects. In this approximation, the electronic structure of the system is calculated using quantum mechanical calculations, and the nuclear motion is treated classically.
Boundary Conditions refer to the conditions imposed on a system to simula… #
Related terms include periodic boundary conditions and free boundary conditions. In Molecular Dynamics Simulations, boundary conditions are used to simulate the behavior of a system in a specific environment.
Car #
Parrinello Molecular Dynamics is a type of molecular dynamics simulation that uses quantum mechanical calculations to calculate the forces on the atoms in a system. Related terms include Ab initio molecular dynamics and quantum molecular dynamics. In this type of simulation, the electronic structure of the system is calculated using quantum mechanical calculations, and the forces on the atoms are calculated using the Hellmann-Feynman theorem.
Classical Molecular Dynamics is a type of molecular dynamics simulation that use… #
Related terms include Newton's equations and force fields. In this type of simulation, the motion of the atoms is calculated using classical mechanics, and the forces on the atoms are calculated using a force field.
Cluster refers to a group of atoms or molecules that are bonded to… #
Related terms include nanoparticle and nanocluster. In Molecular Dynamics Simulations, clusters can be used to model the behavior of small systems or nanoparticles.
Condensed Matter Physics refers to the study of the behavior of solid… #
Related terms include solid state physics and materials science. In Molecular Dynamics Simulations, condensed matter physics is used to study the behavior of solids and liquids.
Constant Pressure Simulation is a type of molecular dynamics simulation that is… #
Related terms include constant volume simulation and isothermal simulation. In this type of simulation, the pressure of the system is kept constant, and the volume of the system is allowed to fluctuate.
Constant Temperature Simulation is a type of molecular dynamics simulation that… #
Related terms include constant energy simulation and isothermal simulation. In this type of simulation, the temperature of the system is kept constant, and the energy of the system is allowed to fluctuate.
Constraint refers to a condition that is imposed on a system to restri… #
Related terms include fixing atoms and restraining forces. In Molecular Dynamics Simulations, constraints are used to simulate the behavior of a system under specific conditions.
Core #
Shell Model is a type of model used to describe the electronic structure of a system. Related terms include core electrons and valence electrons. In this model, the core electrons are treated as a core, and the valence electrons are treated as a shell.
Crystal Structure refers to the arrangement of atoms in a crystalline<… #
Related terms include lattice parameters and space group. In Molecular Dynamics Simulations, the crystal structure of a system can be used to calculate its properties.
Density Functional Theory is a type of quantum mechanical calculation tha… #
Related terms include Kohn-Sham equations and exchange correlation functional. In Molecular Dynamics Simulations, density functional theory is used to calculate the electronic structure of a system.
Density Of States refers to the number of states available to an <… #
Related terms include band structure and electronic structure. In Molecular Dynamics Simulations, the density of states can be used to calculate the properties of a system.
Dipole Moment refers to the measure of the separation of charge… #
Related terms include polarization and electric field. In Molecular Dynamics Simulations, the dipole moment can be used to calculate the properties of a system.
Dispersion Correction refers to a correction that is used to account</… #
Related terms include van der Waals forces and London dispersion forces. In Molecular Dynamics Simulations, dispersion corrections are used to improve the accuracy of the simulations.
Elastic Constants refer to the measure of the stiffness of a mater… #
Related terms include Young's modulus and Poisson ratio. In Molecular Dynamics Simulations, the elastic constants can be used to calculate the properties of a material.
Electron Density refers to the measure of the number of electro… #
Related terms include charge density and spin density. In Molecular Dynamics Simulations, the electron density can be used to calculate the properties of a system.
Electron Transfer refers to the process by which an electron is tr… #
Related terms include charge transfer and redox reaction. In Molecular Dynamics Simulations, electron transfer can be used to simulate the behavior of systems that undergo charge transfer reactions.
Empirical Potential refers to a type of potential that is used to desc… #
Related terms include force field and interatomic potential. In Molecular Dynamics Simulations, empirical potentials are used to calculate the forces on the atoms in a system.
Energy Minimization refers to the process of finding the minimum e… #
Related terms include optimization algorithm and global minimization. In Molecular Dynamics Simulations, energy minimization is used to find the most stable structure of a system.
Ensemble refers to a collection of systems that are used to simula… #
Related terms include canonical ensemble and microcanonical ensemble. In Molecular Dynamics Simulations, ensembles are used to simulate the behavior of systems under specific conditions.
Exchange Correlation Functional refers to a type of functional that is us… #
Related terms include Kohn-Sham equations and density functional theory. In Molecular Dynamics Simulations, exchange correlation functionals are used to calculate the electronic structure of a system.
Force Field refers to a type of potential that is used to describe … #
Related terms include empirical potential and interatomic potential. In Molecular Dynamics Simulations, force fields are used to calculate the forces on the atoms in a system.
Free Energy refers to the measure of the energy available to a sys… #
Related terms include enthalpy and entropy. In Molecular Dynamics Simulations, the free energy can be used to calculate the properties of a system.
Gas Phase Simulation is a type of molecular dynamics simulation that is used to… #
Related terms include liquid phase simulation and solid phase simulation. In this type of simulation, the system is simulated in the gas phase, and the behavior of the system is studied.
Global Minimization refers to the process of finding the global mi… #
Related terms include optimization algorithm and energy minimization. In Molecular Dynamics Simulations, global minimization is used to find the most stable structure of a system.
Hamiltonian refers to the operator that is used to describe the <i… #
Related terms include quantum mechanics and Schrodinger equation. In Molecular Dynamics Simulations, the Hamiltonian is used to calculate the electronic structure of a system.
Hellmann #
Feynman Theorem refers to a theorem that is used to calculate the forces on the atoms in a system. Related terms include Ab initio molecular dynamics and quantum molecular dynamics. In Molecular Dynamics Simulations, the Hellmann-Feynman theorem is used to calculate the forces on the atoms in a system.
Hybrid Functional refers to a type of functional that is used to combi… #
Related terms include Kohn-Sham equations and density functional theory. In Molecular Dynamics Simulations, hybrid functionals are used to calculate the electronic structure of a system.
Interatomic Potential refers to a type of potential that is used to de… #
Related terms include force field and empirical potential. In Molecular Dynamics Simulations, interatomic potentials are used to calculate the forces on the atoms in a system.
Interface refers to the boundary between two or more phases or … #
Related terms include surface tension and interfacial energy. In Molecular Dynamics Simulations, interfaces can be used to study the behavior of systems at the boundary between two or more phases.
Ionization Energy refers to the energy required to remove an el… #
Related terms include electron affinity and ionization potential. In Molecular Dynamics Simulations, the ionization energy can be used to calculate the properties of a system.
Kohn #
Sham Equations refer to a set of equations that are used to describe the electronic structure of a system. Related terms include density functional theory and exchange correlation functional. In Molecular Dynamics Simulations, the Kohn-Sham equations are used to calculate the electronic structure of a system.
Lattice Parameters refer to the parameters that are used to describe</… #
Related terms include crystal structure and space group. In Molecular Dynamics Simulations, the lattice parameters can be used to calculate the properties of a system.
Liquid Phase Simulation is a type of molecular dynamics simulation that is used… #
Related terms include gas phase simulation and solid phase simulation. In this type of simulation, the system is simulated in the liquid phase, and the behavior of the system is studied.
Local Density Approximation refers to a type of approximation that is use… #
Related terms include Kohn-Sham equations and density functional theory. In Molecular Dynamics Simulations, the local density approximation is used to calculate the electronic structure of a system.
Magnetic Moment refers to the measure of the magnetic properties o… #
Related terms include spin density and orbital moment. In Molecular Dynamics Simulations, the magnetic moment can be used to calculate the properties of a system.
Molecular Dynamics Simulation is a type of simulation that is used to … #
Related terms include classical molecular dynamics and quantum molecular dynamics. In this type of simulation, the motion of the atoms in a system is calculated using classical mechanics or quantum mechanics.
Molecular Orbital refers to a mathematical function that is used to de… #
Related terms include atomic orbital and molecular orbital theory. In Molecular Dynamics Simulations, molecular orbitals are used to calculate the electronic structure of a system.
Monte Carlo Simulation is a type of simulation that is used to study</… #
Related terms include importance sampling and Markov chain Monte Carlo. In Molecular Dynamics Simulations, Monte Carlo simulations can be used to calculate the properties of a system.
Nanostructure refers to a structure that has a size on the nano… #
Related terms include nanoparticle and nanomaterial. In Molecular Dynamics Simulations, nanostructures can be used to study the behavior of systems at the nanoscale.
Non #
Adiabatic Effects refer to the effects that occur when the electronic degrees of freedom are not separated from the nuclear degrees of freedom. Related terms include adiabatic approximation and non adiabatic coupling. In Molecular Dynamics Simulations, non-adiabatic effects can be important for systems with high temperatures or large amplitude motions.
Nuclear Magnetic Resonance refers to a technique that is used to study… #
Related terms include magnetic moment and nuclear spin. In Molecular Dynamics Simulations, nuclear magnetic resonance can be used to calculate the properties of a system.
Optimization Algorithm refers to a method that is used to find the… #
Related terms include energy minimization and global minimization. In Molecular Dynamics Simulations, optimization algorithms are used to find the most stable structure of a system.
Pair Correlation Function refers to a function that is used to describ… #
Related terms include radial distribution function and structure factor. In Molecular Dynamics Simulations, the pair correlation function can be used to calculate the properties of a system.
Path Integral Molecular Dynamics is a type of molecular dynamics simulation that… #
Related terms include quantum molecular dynamics and path integral Monte Carlo. In this type of simulation, the motion of the atoms in a system is calculated using path integral methods.
Periodic Boundary Conditions refer to a type of boundary condition that i… #
Related terms include free boundary conditions and fixed boundary conditions. In Molecular Dynamics Simulations, periodic boundary conditions are used to simulate the behavior of a system in a periodic environment.
Phonon refers to a quantum of sound in a solid #
Related terms include phonon dispersion and phonon density of states. In Molecular Dynamics Simulations, phonons can be used to calculate the properties of a system.
Potential Energy Surface refers to the surface that is used to describ… #
Related terms include force field and interatomic potential. In Molecular Dynamics Simulations, the potential energy surface is used to calculate the forces on the atoms in a system.
Quantum Molecular Dynamics is a type of molecular dynamics simulation that is us… #
Related terms include Ab initio molecular dynamics and path integral molecular dynamics. In this type of simulation, the motion of the atoms in a system is calculated using quantum mechanics.
Radial Distribution Function refers to a function that is used to desc… #
Related terms include pair correlation function and structure factor. In Molecular Dynamics Simulations, the radial distribution function can be used to calculate the properties of a system.
Reaction Coordinate refers to a coordinate that is used to describe</b… #
Related terms include reaction path and transition state. In Molecular Dynamics Simulations, the reaction coordinate can be used to study the behavior of a system during a reaction.
Relaxation Time refers to the time it takes for a system to relax … #
Related terms include time constant and relaxation dynamics. In Molecular Dynamics Simulations, the relaxation time can be used to study the behavior of a system over time.
Schrödinger Equation refers to a equation that is used to describe … #
Related terms include Hamiltonian and wave function. In Molecular Dynamics Simulations, the Schrödinger equation is used to calculate the electronic structure of a system.
Self #
Consistent Field refers to a method that is used to solve the Schrödinger equation for a system. Related terms include Hartree-Fock method and density functional theory. In Molecular Dynamics Simulations, the self-consistent field method is used to calculate the electronic structure of a system.
Simulation Cell refers to the region of space that is used to simulate… #
Related terms include periodic boundary conditions and boundary conditions. In Molecular Dynamics Simulations, the simulation cell is used to define the region of space where the simulation is performed.
Solvent refers to a substance that is used to dissolve another sub… #
Related terms include solution and solubility. In Molecular Dynamics Simulations, solvents can be used to study the behavior of systems in solution.
Spin Density refers to the measure of the spin properties of a sys… #
Related terms include magnetic moment and orbital moment. In Molecular Dynamics Simulations, the spin density can be used to calculate the properties of a system.
Structural Optimization refers to the process of finding the most … #
Related terms include energy minimization and global minimization. In Molecular Dynamics Simulations, structural optimization is used to find the most stable structure of a system.
Surface Energy refers to the energy associated with the surface of… #
Related terms include surface tension and interfacial energy. In Molecular Dynamics Simulations, the surface energy can be used to calculate the properties of a system.
Thermal Conductivity refers to the measure of the ability of a sys… #
Related terms include thermal diffusivity and heat transfer. In Molecular Dynamics Simulations, the thermal conductivity can be used to calculate the properties of a system.
Thermodynamic Properties refer to the properties of a system that are rel… #
Related terms include free energy and entropy. In Molecular Dynamics Simulations, thermodynamic properties can be used to calculate the properties of a system.
Time #
Dependent Density Functional Theory refers to a type of density functional theory that is used to describe the time-evolution of a system. Related terms include time-dependent Schrödinger equation and density functional theory. In Molecular Dynamics Simulations, time-dependent density functional theory is used to calculate the electronic structure of a system.
Transition State refers to the state of a system that is associated</b… #
Related terms include reaction coordinate and activation energy. In Molecular Dynamics Simulations, the transition state can be used to study the behavior of a system during a reaction.
Vibrational Spectrum refers to the spectrum of vibrational modes o… #
Related terms include infrared spectrum and Raman spectrum. In Molecular Dynamics Simulations, the vibrational spectrum can be used to calculate the properties of a system.
Wave Function refers to a mathematical function that is used to descri… #
Related terms include Schrödinger equation and density functional theory. In Molecular Dynamics Simulations, the wave function is used to calculate the electronic structure of a system.
X-Ray Absorption Spectroscopy refers to a technique that is used to st… #
Related terms include x-ray diffraction and x-ray photoelectron spectroscopy. In Molecular Dynamics Simulations, x-ray absorption spectroscopy can be used to calculate the properties of a system.
Yukawa Potential refers to a type of potential that is used to describ… #
Related terms include screened Coulomb potential and Debye screening length. In Molecular Dynamics Simulations, the Yukawa potential can be used to calculate the forces on the atoms in a system.
Zero #
Point Energy refers to the energy that is associated with the zero-point motion of a system. Related terms include quantum fluctuations and thermal fluctuations. In Molecular Dynamics Simulations, the zero-point energy can be used to calculate the properties of a system.