Sampling algorithms, potential energy surfaces

Genetic algorithm (GA) is a kind of widely used method to determine the global minimum structure of a cluster. It can sample the potential energy surface efficiently and hop from one region of the PES to another region rather easily. It is inspired by Darwinian evolution theory that only the fittest individuals can survive. The basic philosophy of GA is to mimic the natural selection and evolution processes in nature. The essential idea of GA procedure is to allow a population of a number of individual candidates to evolve under a given selection rule that maximizes the fitness function. 

HyperChem provides three types of potential energy surface sampling algorithms. These are found in the HyperChem Compute menu Single Point, Geometry Optimization, and Molecular Dynamics. 

Keywords Ab initio molecular dynamics simulations Always stable predictor-corrector algorithm Associated liquids Basis set Bom-Oppenheimer molecular dynamics simulations Car-Parrinello molecular dynamics simulations Catalysis Collective variable Discrete variable representation Dispersion Effective core potential Enhanced sampling Fictitious mass First-principles molecular dynamics simulations Free energy surface Hartree-Fock exchange Ionic liquids Linear scaling Metadynamics Nudged elastic band Numerically tabulated atom-centered orbitals Plane waves Pseudopotential Rare event Relativistic electronic structure Retention potential Self consistent field SHAKE algorithm ... 

A force field can be coupled with molecular dynamics (MD) algorithms to sample local conformational space around the energy minimum of a macro-molecule. An MD algorithm involves the numerical integration of Newton s equation s of motion, where the acceleration of a particle is a = Fj/w, and the force Fj is the negative gradient of the potential surface. New atomic positions and velocities are calculated repeatedly with a small time step on the order of 10 " sec (1 fsec). The resulting set of time dependent coordinates is known as a trajectory. 

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