Molecular dynamics (MD) simulations capture atomic and molecular motion based on Newtonian equations of motion and empirical potential functions that define the interactions between simulated particles. The latter is described by a force field, which is a collection of physically consistent equations and semi-empirical parameters that characterize all interactions in a particular system. The dependence of a system's energy on its particle coordinates is expressed mathematically as the force field. It consists of an analytical representation of the interatomic potential energy and a set of input parameters. In most cases, the atomic or molecular characteristics of a small molecule are matched to estimated quantum mechanical or experimental observations to produce the force field parameters.
Fig 1. Classical force fields used for MD simulations: (Right) potential energy terms in a force field; and (Left) energy function used to derive atomic forces for molecular movement. (Chang C-E. A, et al. 2016)
Molecules are simply defined as a set of atoms held together by simple elastic (harmonic) forces, and the force field replaces the real potential energy with a simplified model that works in the simulation region. Alfa Chemistry offers research services for MD simulation using a range of force fields to study molecular dynamics. Modern techniques and highly qualified computational chemists are available on our platform to advance the chemical and pharmaceutical industries. We promise to give you the finest service possible.
Assisted Model Building with Energy Refinement (AMBER) is a set of molecular force fields for molecular dynamics of biomolecules, with a wide range of applications in the field of biomolecular simulation calculations. The strength of the AMBER force field lies in the computation of biomolecules. Currently, AMBER force fields are implemented in many common computational software programs. Alfa Chemistry is able to use AMBER Force Field to provide MD simulation services to its customers.
Optimized Potentials for Liquid Simulations (OPLS) is a set of molecular force fields for molecular dynamics of liquid systems, which are widely used in the simulation of organic small molecules, protein condensed phases, etc. OPLS force fields are developed specifically for liquid systems such as peptides, proteins, nucleic acids, organic solvents, etc. and are generally used in conjunction with Alfa Chemistry can provide customers with MD simulation services through the OPLS force field.
Groningen Molecular Simulation (GROMOS) is one of the most common force fields used in today's biomolecular simulations. GROMOS force fields are integrated atomic force fields whose force parameters are derived by fitting experimental data to the thermodynamic properties of pure or mixed fluid systems in the condensed state. Alfa Chemistry can provide customers with MD simulation services through GROMOS force fields.
Alfa Chemistry provides global customers with fast, professional, high-quality MD simulation services at competitive prices to reduce the cost of late-stage experiments. This service is a personalized and customized innovative scientific research service. We need to evaluate each project before we can determine the corresponding analysis plan and price. If you are interested in our services, please contact us for more details.