Literature DB >> 23678385

λ-Meta Dynamics Approach To Compute Absolute Solvation Free Energy.

Pan Wu1, Xiangqian Hu, Weitao Yang.   

Abstract

We present a new approach to combine λ dynamics with meta-dynamics (named λ-meta dynamics) to compute free energy surface with respect to λ. Particularly, the λ-meta dynamics method extends meta-dynamics to a single virtual variable λ, i.e., the coupling parameter between solute and solvent, to compute absolute solvation free energy as an exemplary application. We demonstrate that λ-meta dynamics simulations can recover the accurate potential of mean force surface with respect to λ compared to the benchmark results from traditional λ-dynamics with umbrella sampling. The solvation free energy results for five small organic molecules from λ-meta dynamics simulations using the same filling scheme show that the statistical errors are within ±0.5 kcal/mol. The new λ-meta dynamics method is general and other variables such as order parameters to describe conformational changes can be easily combined with λ-meta dynamics. This should allow for efficient samplings on high-dimension free energy landscapes.

Entities:  

Keywords:  Meta-dynamics; QM/MM; solvation free energy; λ dynamics; λ-meta dynamics

Year:  2011        PMID: 23678385      PMCID: PMC3652470          DOI: 10.1021/jz200808x

Source DB:  PubMed          Journal:  J Phys Chem Lett        ISSN: 1948-7185            Impact factor:   6.475


  27 in total

Review 1.  Generalized born models of macromolecular solvation effects.

Authors:  D Bashford; D A Case
Journal:  Annu Rev Phys Chem       Date:  2000       Impact factor: 12.703

2.  A fuzzy ARTMAP-based quantitative structure-property relationship (QSPR) for the Henry's law constant of organic compounds.

Authors:  Denise Yaffe; Yoram Cohen; Gabriela Espinosa; Alex Arenas; Francesc Giralt
Journal:  J Chem Inf Comput Sci       Date:  2003 Jan-Feb

3.  Escaping free-energy minima.

Authors:  Alessandro Laio; Michele Parrinello
Journal:  Proc Natl Acad Sci U S A       Date:  2002-09-23       Impact factor: 11.205

Review 4.  The many roles of computation in drug discovery.

Authors:  William L Jorgensen
Journal:  Science       Date:  2004-03-19       Impact factor: 47.728

5.  Prediction of SAMPL2 aqueous solvation free energies and tautomeric ratios using the SM8, SM8AD, and SMD solvation models.

Authors:  Raphael F Ribeiro; Aleksandr V Marenich; Christopher J Cramer; Donald G Truhlar
Journal:  J Comput Aided Mol Des       Date:  2010-04-01       Impact factor: 3.686

6.  Computations of Absolute Solvation Free Energies of Small Molecules Using Explicit and Implicit Solvent Model.

Authors:  Devleena Shivakumar; Yuqing Deng; Benoît Roux
Journal:  J Chem Theory Comput       Date:  2009-03-24       Impact factor: 6.006

7.  Prediction of Absolute Solvation Free Energies using Molecular Dynamics Free Energy Perturbation and the OPLS Force Field.

Authors:  Devleena Shivakumar; Joshua Williams; Yujie Wu; Wolfgang Damm; John Shelley; Woody Sherman
Journal:  J Chem Theory Comput       Date:  2010-04-14       Impact factor: 6.006

8.  Assessing the accuracy of metadynamics.

Authors:  Alessandro Laio; Antonio Rodriguez-Fortea; Francesco Luigi Gervasio; Matteo Ceccarelli; Michele Parrinello
Journal:  J Phys Chem B       Date:  2005-04-14       Impact factor: 2.991

9.  Metadynamics as a tool for exploring free energy landscapes of chemical reactions.

Authors:  Bernd Ensing; Marco De Vivo; Zhiwei Liu; Preston Moore; Michael L Klein
Journal:  Acc Chem Res       Date:  2006-02       Impact factor: 22.384

10.  Relative solvation free energies calculated using an ab initio QM/MM-based free energy perturbation method: dependence of results on simulation length.

Authors:  M Rami Reddy; Mark D Erion
Journal:  J Comput Aided Mol Des       Date:  2009-09-17       Impact factor: 3.686

View more
  3 in total

1.  Molecular Dynamics Simulations with Quantum Mechanics/Molecular Mechanics and Adaptive Neural Networks.

Authors:  Lin Shen; Weitao Yang
Journal:  J Chem Theory Comput       Date:  2018-02-26       Impact factor: 6.006

2.  Solvation Free Energy Calculations with Quantum Mechanics/Molecular Mechanics and Machine Learning Models.

Authors:  Pan Zhang; Lin Shen; Weitao Yang
Journal:  J Phys Chem B       Date:  2019-01-15       Impact factor: 2.991

3.  Driven Metadynamics: Reconstructing Equilibrium Free Energies from Driven Adaptive-Bias Simulations.

Authors:  Mahmoud Moradi; Emad Tajkhorshid
Journal:  J Phys Chem Lett       Date:  2013-05-17       Impact factor: 6.475

  3 in total

北京卡尤迪生物科技股份有限公司 © 2022-2023.