Molecular dynamics (MD) is a computer simulation method for analyzing the physical movements of atoms and molecules. The atoms and molecules are allowed to interact for a fixed period of time, giving a view of the dynamic "evolution" of the system. In the most common version, the trajectories of atoms and molecules are determined by numerically solving Newton's equations of motion for a system of interacting particles, where forces between the particles and their potential energies are often calculated using interatomic potentials or molecular mechanical force fields. The method is applied mostly in chemical physics, materials science, and biophysics.
Chemistry at Harvard Macromolecular Mechanics (CHARMM) is the name of a widely used set of force fields for molecular dynamics, and the name for the molecular dynamics simulation and analysis computer software package associated with them. The CHARMM Development Project involves a worldwide network of developers working with Martin Karplus and his group at Harvard to develop and maintain the CHARMM program. Licenses for this software are available, for a fee, to people and groups working in academia.
Molecular mechanics uses classical mechanics to model molecular systems. The Born–Oppenheimer approximation is assumed valid and the potential energy of all systems is calculated as a function of the nuclear coordinates using force fields. Molecular mechanics can be used to study molecule systems ranging in size and complexity from small to large biological systems or material assemblies with many thousands to millions of atoms.
Molecular modelling encompasses all methods, theoretical and computational, used to model or mimic the behaviour of molecules. The methods are used in the fields of computational chemistry, drug design, computational biology and materials science to study molecular systems ranging from small chemical systems to large biological molecules and material assemblies. The simplest calculations can be performed by hand, but inevitably computers are required to perform molecular modelling of any reasonably sized system. The common feature of molecular modelling methods is the atomistic level description of the molecular systems. This may include treating atoms as the smallest individual unit, or explicitly modelling protons and neutrons with its quarks, anti-quarks and gluons and electrons with its photons.
In the context of chemistry, molecular physics and physical chemistry and molecular modelling, a force field is a computational model that is used to describe the forces between atoms within molecules or between molecules as well as in crystals. Force fields are a variety of interatomic potentials. More precisely, the force field refers to the functional form and parameter sets used to calculate the potential energy of a system of the atomistic level. Force fields are usually used in molecular dynamics or Monte Carlo simulations. The parameters for a chosen energy function may be derived from classical laboratory experiment data, calculations in quantum mechanics, or both. Force fields utilize the same concept as force fields in classical physics, with the main difference 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 coordinates.
Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) is a molecular dynamics program from Sandia National Laboratories. 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.
Tinker, previously stylized as TINKER, is a suite of computer software applications for molecular dynamics simulation. The codes provide a complete and general set of tools for molecular mechanics and molecular dynamics, with some special features for biomolecules. The core of the software is a modular set of callable routines which allow manipulating coordinates and evaluating potential energy and derivatives via straightforward means.
Molecular design software is notable software for molecular modeling, that provides special support for developing molecular models de novo.
Molecular modeling on GPU is the technique of using a graphics processing unit (GPU) for molecular simulations.
Molecular Dynamics of Mixtures (MDynaMix) is a computer software package for general purpose molecular dynamics to simulate mixtures of molecules, interacting by AMBER- and CHARMM-like force fields in periodic boundary conditions. Algorithms are included for NVE, NVT, NPT, anisotropic NPT ensembles, and Ewald summation to treat electrostatic interactions. The code was written in a mix of Fortran 77 and 90. The package runs on Unix and Unix-like (Linux) workstations, clusters of workstations, and on Windows in sequential mode.
CP2K is a freely available (GPL) quantum chemistry and solid state physics program package, written in Fortran 2008, to perform atomistic simulations of solid state, liquid, molecular, periodic, material, crystal, and biological systems. It provides a general framework for different methods: density functional theory (DFT) using a mixed Gaussian and plane waves approach (GPW) via LDA, GGA, MP2, or RPA levels of theory, classical pair and many-body potentials, semi-empirical and tight-binding Hamiltonians, as well as Quantum Mechanics/Molecular Mechanics (QM/MM) hybrid schemes relying on the Gaussian Expansion of the Electrostatic Potential (GEEP). The Gaussian and Augmented Plane Waves method (GAPW) as an extension of the GPW method allows for all-electron calculations. CP2K can do simulations of molecular dynamics, metadynamics, Monte Carlo, Ehrenfest dynamics, vibrational analysis, core level spectroscopy, energy minimization, and transition state optimization using NEB or dimer method.
This is a list of notable computer programs that are used for nucleic acids simulations.
Abalone is a general purpose molecular dynamics and molecular graphics program for simulations of bio-molecules in a periodic boundary conditions in explicit or in implicit water models. Mainly designed to simulate the protein folding and DNA-ligand complexes in AMBER force field.
Biochemical and Organic Simulation System (BOSS) is a general-purpose molecular modeling program that performs molecular mechanics calculations, Metropolis Monte Carlo statistical mechanics simulations, and semiempirical Austin Model 1 (AM1), PM3, and PDDG/PM3 quantum mechanics calculations. The molecular mechanics calculations cover energy minimizations, normal mode analysis and conformational searching with the Optimized Potentials for Liquid Simulations (OPLS) force fields. BOSS is developed by Prof. William L. Jorgensen at Yale University, and distributed commercially by Cemcomco, LLC and Schrödinger, Inc.
Ascalaph Designer is a computer program for general purpose molecular modelling for molecular design and simulations. It provides a graphical environment for the common programs of quantum and classical molecular modelling ORCA, NWChem, Firefly, CP2K and MDynaMix . The molecular mechanics calculations cover model building, energy optimizations and molecular dynamics. Firefly covers a wide range of quantum chemistry methods. Ascalaph Designer is free and open-source software, released under the GNU General Public License, version 2 (GPLv2).
MacroModel is a computer program for molecular modelling of organic compounds and biopolymers. It features various chemistry force fields, plus energy minimizing algorithms, to predict geometry and relative conformational energies of molecules. MacroModel is maintained by Schrödinger, LLC.
MBN Explorer is a software package for molecular dynamics simulations, structure optimization and kinetic Monte Carlo simulations. It is designed for multiscale computational analysis of structure and dynamics of atomic clusters and nanoparticles, biomolecules and nanosystems, nanostructured materials, different states of matter and various interfaces. The software has been developed by MBN Research Center.