Variational approach for nonpolar solvation analysis
نویسندگان
چکیده
منابع مشابه
Coupling the Level-Set Method with Molecular Mechanics for Variational Implicit Solvation of Nonpolar Molecules.
We construct a variational explicit-solute implicit-solvent model for the solvation of molecules. Central in this model is an effective solvation free-energy functional that depends solely on the position of solute-solvent interface and solute atoms. The total free energy couples altogether the volume and interface energies of solutes, the solute-solvent van der Waals interactions, and the solu...
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We incorporate the Poisson-Boltzmann (PB) theory of electrostatics into our variational implicit-solvent model (VISM) for the solvation of charged molecules in an aqueous solvent. In order to numerically relax the VISM free-energy functional by our level-set method, we develop highly accurate methods for solving the dielectric PB equation and for computing the dielectric boundary force. We also...
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Accurate description of the solvent environment is critical in computer simulations of protein structure and dynamics. An implicit treatment of solvent aims to capture the mean influence of water molecules on the solute via direct estimation of the solvation free energy. It has emerged as a powerful alternative to explicit solvent, and provides a favorable compromise between computational cost ...
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Continuum solvation methods are frequently used to increase the efficiency of computational methods to estimate free energies. In this paper, we have evaluated how well such methods estimate the nonpolar solvation free-energy change when a ligand binds to a protein. Three different continuum methods at various levels of approximation were considered, viz., the polarized continuum model (PCM), a...
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A level-set method is developed for numerically capturing the equilibrium solute-solvent interface that is defined by the recently proposed variational implicit solvent model [Dzubiella, Swanson, and McCammon, Phys. Rev. Lett. 104, 527 (2006); J. Chem. Phys. 124, 084905 (2006)]. In the level-set method, a possible solute-solvent interface is represented by the zero level set (i.e., the zero lev...
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ژورنال
عنوان ژورنال: The Journal of Chemical Physics
سال: 2012
ISSN: 0021-9606,1089-7690
DOI: 10.1063/1.4745084