title: Hydration Free Energy from Orthogonal Space Random Walk and Polarizable Force Field.
abstract: 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 which 15 are positively charged and five are neutral. The calculated hydration free energies of these molecules are compared with the results obtained from the Bennett acceptance ratio method using the same force field, and overall an excellent agreement is obtained. The convergence and the efficiency of the OSRW are also discussed and compared with BAR. Combining enhanced sampling techniques such as OSRW with polarizable force fields is very promising for achieving both accuracy and efficiency in general free energy calculations.
authors.affiliation: Department of Biomedical Engineering and Department of Physics, The University of Texas at Austin , Austin, Texas 78712, United States.
authors.forename: Jayvee R
authors.initials: JR
authors.lastname: Abella
authors.affiliation: Department of Biomedical Engineering and Department of Physics, The University of Texas at Austin , Austin, Texas 78712, United States.
authors.forename: Sara Y
authors.initials: SY
authors.lastname: Cheng
authors.affiliation: Department of Biomedical Engineering and Department of Physics, The University of Texas at Austin , Austin, Texas 78712, United States.
authors.forename: Qiantao
authors.initials: Q
authors.lastname: Wang
authors.affiliation: Institute of Molecular Biophysics and Department of Chemistry and Biochemistry, Florida State University , Tallahassee, Florida 32306, United States ; Institute of Molecular Biophysics and Department of Chemistry and Biochemistry, Florida State University , Tallahassee, Florida 32306, United States.
authors.forename: Wei
authors.initials: W
authors.lastname: Yang
authors.affiliation: Department of Biomedical Engineering and Department of Physics, The University of Texas at Austin , Austin, Texas 78712, United States.
authors.forename: Pengyu
authors.initials: P
authors.lastname: Ren