Hybrid monte carlo reaction method

Moreover, we have recently proposed and developed the hybrid Monte Carlo (MC)/Molecular Dynamics (MD) reaction method [70] to realize the practical atomistic simulation method for a massive complex chemical reacting systems. The concept of the hybrid MC/MD reaction method is shown in Fig. 8.16. First, we execute MD simulation in the region R until one (or some) pair of atoms meets the necessary conditions and select (instantaneous) configuration state r. Next, one of pairs is virtually reacted to generate a (instantaneous) configuration state s, relaxing... 

The Intention of this volume is to give a flavour of the types of problems in biochemistry that theoretical calculations can solve at present, and to illustrate the tremendous predictive power these approaches possess. With these aspects in mind, I have tried to gather some of the leading scientists in the field of theoretical/computational biochemistry and let them present their work. You will hence find a wide range of computational approaches, from classical MD and Monte Carlo methods, via semi-empirical and DFT approaches on isolated model systems, to Car-Parrinello QM-MD and novel hybrid QM/MM studies. The systems investigated also cover a broad range from membrane-bound proteins to various types of enzymatic reactions as well as inhibitor studies, cofactor properties, solvent effects, transcription and radiation damage to DNA. 

In recent years, there have been many attempts to combine the best of both worlds. Continuum solvent models (reaction field and variations thereof) are very popular now in quantum chemistry but they do not solve all problems, since the environment is treated in a static mean-field approximation. The Car-Parrinello method has found its way into chemistry and it is probably the most rigorous of the methods presently feasible. However, its computational cost allows only the study of systems of a few dozen atoms for periods of a few dozen picoseconds. Semiempirical cluster calculations on chromophores in solvent structures obtained from classical Monte Carlo calculations are discussed in the contribution of Coutinho and Canuto in this volume. In the present article, we describe our attempts with so-called hybrid or quantum-mechanical/molecular-mechanical (QM/MM) methods. These concentrate on the part of the system which is of primary interest (the reactants or the electronically excited solute, say) and treat it by semiempirical quantum chemistry. The rest of the system (solvent, surface, outer part of enzyme) is described by a classical force field. With this, we hope to incorporate the essential influence of the in itself uninteresting environment on the dynamics of the primary system. The approach lacks the rigour of the Car-Parrinello scheme but it allows us to surround a primary system of up to a few dozen atoms by an environment of several ten thousand atoms and run the whole system for several hundred thousand time steps which is equivalent to several hundred picoseconds. 

The work described in Refs. 5 and 17 indicated that hybrid potentials could describe reaction processes in solution. However, it is only with the work of Gao that the real utility of this approach has become apparent. He and his co-workers have developed a hybrid potential that combines the AMI/MNDO semiempirical method with a force field similar to the OPLS force field of Jorgensen and with it they have studied a very wide range of solution phenomena in combination with Monte Carlo simulation techniques. As Gao has recently published two excellent reviews of hybrid potentials which include discussion of his own work only a few brief details will be given here. 

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