Models for biomolecular simulations

B Roux, T Simonson, eds. Implicit Solvent Models for Biomolecular Simulations. Special Issue of Biophys Chem Amsterdam Elsevier, 1999. 

Marrink, S.J., Risselada, H.J., Yefimov, S., Tieleman, D.P., de Vries, A.H. The MARTINI force field coarse grained model for biomolecular simulations. J. Phys. Chem. B 2007, 111, 7812-24. 

H.W. Horn et al., Development of an improved four-site water model for biomolecular simulations TIP4P-Ew. J. Chem. Phys. 120, 9665 (2004)... 

Benoit Roux and Thomas Simonson, Special Issue Implicit Solvent Models for Biomolecular Simulations, in Biopbys. Chem., 78 (1-2), 1999. 

The total electric field, E, is composed of the external electric field from the permanent charges E° and the contribution from other induced dipoles. This is the basis of most polarizable force fields currently being developed for biomolecular simulations. In the present chapter an overview of the formalisms most commonly used for MM force fields will be presented. It should be emphasized that this chapter is not meant to provide a broad overview of the field but rather focuses on the formalisms of the induced dipole, classical Drude oscillator and fluctuating charge models and their development in the context of providing a practical polarization model for molecular simulations of biological macromolecules [12-21], While references to works in which the different methods have been developed and applied are included throughout the text, the major discussion of the implementation of these models focuses... 

Noid, W. G. (2012J. Systematic methods for structurally consistent coarsegrained models, in Biomolecular Simulations (Humana Press, Totowa, NJ), pp. 487-531. 

Ren and coworkers report a new polarizable development and parameterization of their atomic multipole-based optimized energetics for biomolecular simulation, AMOEBA2013 force field for proteins. It uses atomic multipole-based electrostatics and has explicit treatment of dipole polarization. Based on a mutual induction model with Thole damping it describes both intra- and intermolecular polarization. 

In the context of molecular simulation, particularly biomolecular modelling, a critical aspect for numerical simulation is the presence of long-range Coulombic forces which render the force computations much more costly... 

Proper condensed phase simulations require that the non-bond interactions between different portions of the system under study be properly balanced. In biomolecular simulations this balance must occur between the solvent-solvent (e.g., water-water), solvent-solute (e.g., water-protein), and solute-solute (e.g., protein intramolecular) interactions [18,21]. Having such a balance is essential for proper partitioning of molecules or parts of molecules in different environments. For example, if the solvent-solute interaction of a glutamine side chain were overestimated, there would be a tendency for the side chain to move into and interact with the solvent. The first step in obtaining this balance is the treatment of the solvent-solvent interactions. The majority of biomolecular simulations are performed using the TIP3P [81] and SPC/E [82] water models. 

In this chapter we provide an introductory overview of the imphcit solvent models commonly used in biomolecular simulations. A number of questions concerning the formulation and development of imphcit solvent models are addressed. In Section II, we begin by providing a rigorous fonmilation of imphcit solvent from statistical mechanics. In addition, the fundamental concept of the potential of mean force (PMF) is introduced. In Section III, a decomposition of the PMF in terms of nonpolar and electrostatic contributions is elaborated. Owing to its importance in biophysics. Section IV is devoted entirely to classical continuum electrostatics. For the sake of completeness, other computational... 

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