Self-consistent simulation programs

The self-consistent nature of the simulation approaches described in this chapter requires frequent solutions of Poisson s equation the potential profiles from one step to the next are very similar to each other because the changes in the charge distribution between two consecutive solutions are very small (but very important for the particle dynamics). The current potential profile can thus generally be used as a good initial guess for the next solution, which makes iterative methods a natural choice within the framework of self-consistent simulation programs. In addition, memory issues (other than pure performance) make the choice of iterative methods appealing in the field of ion channel simulations. 

Continued Quantum and Molecular Mechanical Simulations, In this technique, a molecular dynamics simulation includes the treatment of some part of the system wilh a quantum mechanical technique. This approach. yMf.MM. is similar to programs that Use quantum mechanical methods to treat the n-systems of the structures in question separately from the sigma framework. The results are combined ai ihe end to render a slructure which is optimized and energy-refined in satisfy both self-consistent field (SCF) and force field energy convergence. 

The Vienna Ab Initio Simulation Package (VASP) program33,34 was developed to carry out calculations to obtain the fluctuation trajectory of the selected models. The VASP program uses a rather traditional self-consistency scheme to evaluate the instantaneous electronic ground-state at each molecular dynamics (MD) step so that the wavefunction can be converged to the Born-Oppenheimer surface at each time-step. 

SCF-MI (Self Consistent Field for Molecular Interactions) and non orthogonal Cl were used to determine a water-water interaction potential, from which BSSE is excluded in an a priori fashion. The new potential has been employed in molecular dynamics simulation of liquid water at 25°C. The simulations were performed using MOTECC suite of programs. The results were compared with experimental data for water in the liquid phase, and good accordance was found, both in radial distribution functions and thermodynamic properties, as well as in geometric parameters. 

AMI AMBER A Program for Simulation of Biological and Organic Molecules CHARMM The Energy Function and Its Parameterization Combined Quantum Mechanics and Molecular Mechanics Approaches to Chemical and Biochemical Reactivity Density Functional Theory (DFT), Hartree-Fock (HF), and the Self-consistent Field Divide and Conquer for Semiempirical MO Methods Electrostatic Catalysis Force Fields A General Discussion Force Fields CFF GROMOS Force Field Hybrid Methods Hybrid Quantum Mechanical/Molecular Mechanical (QM/MM) Methods Mixed Quantum-Classical Methods MNDO MNDO/d Molecular Dynamics Techniques and Applications to Proteins OPLS Force Fields Parameterization of Semiempirical MO Methods PM3 Protein Force Fields Quantum Mechanical/Molecular Mechanical (QM/MM) Coupled Potentials Quantum Mecha-nics/Molecular Mechanics (QM/MM) SINDOI Parameterization and Application. 

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