Hydration Free Energy from Orthogonal Space Random Walk and Polarizable Force Field
نویسندگان
چکیده
منابع مشابه
Hydration Free Energy from Orthogonal Space Random Walk and Polarizable Force Field
The orthogonal space random walk (OSRW) method has shown enhanced sampling efficiency in free energy calculations from previous studies. In this study, the implementation of OSRW in accordance with the polarizable AMOEBA force field in TINKER molecular modeling software package is discussed and subsequently applied to the hydration free energy calculation of 20 small organic molecules, among wh...
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Hydration free energy (HFE) calculations are often used to assess the performance of biomolecular force fields and the quality of assigned parameters. The AMOEBA polarizable force field moves beyond traditional pairwise additive models of electrostatics and may be expected to improve upon predictions of thermodynamic quantities such as HFEs over and above fixed-point-charge models. The recent S...
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In the past few decades, many ingenious efforts have been made in the development of free-energy simulation methods. Because complex systems often undergo nontrivial structural transition during state switching, achieving efficient free-energy calculation can be challenging. As identified earlier, the "Hamiltonian" lagging, which reveals the fact that necessary structural relaxation falls behin...
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Thermodynamic measurements of the solvation of salts and electrolytes are relatively straightforward, but it is not possible to separate total solvation free energies into distinct cation and anion contributions without reference to an additional extrathermodynamic assumption. The present work attempts to resolve this difficulty using molecular dynamics simulations with the AMOEBA polarizable f...
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In Computer-Aided-Drug-Design (CADD), the electrostatic interactions contribute strongly to the interaction between the drug-molecule and the target. Further, the Coulomb term is crucial for calculating the electrostatic contribution to the solvation energy. In spite of this, conventional Force Fields use the obsolete physical concept of point-monopoles (net atomic charges) and thus, are not ab...
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ژورنال
عنوان ژورنال: Journal of Chemical Theory and Computation
سال: 2014
ISSN: 1549-9618,1549-9626
DOI: 10.1021/ct500202q