Design and application of implicit solvent models in biomolecular simulations
نویسندگان
چکیده
منابع مشابه
Implicit Solvent Models for Simulations
A statistical thermodynamic development is given of a new implicit solvent model that avoids the traditional system size limitations of computer simulation of macromolecular solutions with periodic boundary conditions. This implicit solvent model is based upon the quasi-chemical approach, distinct from the common integral equation trunk of the theory of liquid solutions. The idea is geometrical...
متن کاملRecent advances in implicit solvent-based methods for biomolecular simulations.
Implicit solvent-based methods play an increasingly important role in molecular modeling of biomolecular structure and dynamics. Recent methodological developments have mainly focused on the extension of the generalized Born (GB) formalism for variable dielectric environments and accurate treatment of nonpolar solvation. Extensive efforts in parameterization of GB models and implicit solvent fo...
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We present a new hybrid explicit/implicit solvent method for dynamics simulations of macromolecular systems. The method models explicitly the hydration of the solute by either a layer or sphere of water molecules, and the generalized Born (GB) theory is used to treat the bulk continuum solvent outside the explicit simulation volume. To reduce the computational cost, we implemented a multigrid m...
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متن کاملImplicit Solvent Models in Molecular Dynamics Simulations: A Brief Overview
This chapter was originally published in the book Annual Reports in Computational Chemistry, Volume 4. The copy attached is provided by Elsevier for the author’s benefit and for the benefit of the author’s institution, for noncommercial research, and educational use. This includes without limitation use in instruction at your institution, distribution to specific colleagues, and providing a cop...
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ژورنال
عنوان ژورنال: Current Opinion in Structural Biology
سال: 2014
ISSN: 0959-440X
DOI: 10.1016/j.sbi.2014.04.003