Literature DB >> 18715052

Developing ab initio quality force fields from condensed phase quantum-mechanics/molecular-mechanics calculations through the adaptive force matching method.

Omololu Akin-Ojo1, Yang Song, Feng Wang.   

Abstract

A new method called adaptive force matching (AFM) has been developed that is capable of producing high quality force fields for condensed phase simulations. This procedure involves the parametrization of force fields to reproduce ab initio forces obtained from condensed phase quantum-mechanics/molecular-mechanics (QM/MM) calculations. During the procedure, the MM part of the QM/MM is iteratively improved so as to approach ab initio quality. In this work, the AFM method has been tested to parametrize force fields for liquid water so that the resulting force fields reproduce forces calculated using the ab initio MP2 and the Kohn-Sham density functional theory with the Becke-Lee-Yang-Parr (BLYP) and Becke three-parameter LYP (B3LYP) exchange correlation functionals. The AFM force fields generated in this work are very simple to evaluate and are supported by most molecular dynamics (MD) codes. At the same time, the quality of the forces predicted by the AFM force fields rivals that of very expensive ab initio calculations and are found to successfully reproduce many experimental properties. The site-site radial distribution functions (RDFs) obtained from MD simulations using the force field generated from the BLYP functional through AFM compare favorably with the previously published RDFs from Car-Parrinello MD simulations with the same functional. Technical aspects of AFM such as the optimal QM cluster size, optimal basis set, and optimal QM method to be used with the AFM procedure are discussed in this paper.

Entities:  

Year:  2008        PMID: 18715052     DOI: 10.1063/1.2965882

Source DB:  PubMed          Journal:  J Chem Phys        ISSN: 0021-9606            Impact factor:   3.488


  34 in total

1.  Pairwise-additive force fields for selected aqueous monovalent ions from adaptive force matching.

Authors:  Jicun Li; Feng Wang
Journal:  J Chem Phys       Date:  2015-11-21       Impact factor: 3.488

2.  Surface Penetration without Enrichment: Simulations Show Ion Surface Propensities Consistent with Both Elevated Surface Tension and Surface Sensitive Spectroscopy.

Authors:  Jicun Li; Feng Wang
Journal:  J Phys Chem B       Date:  2019-08-13       Impact factor: 2.991

3.  The liquid-vapor equilibria of TIP4P/2005 and BLYPSP-4F water models determined through direct simulations of the liquid-vapor interface.

Authors:  Hongyi Hu; Feng Wang
Journal:  J Chem Phys       Date:  2015-06-07       Impact factor: 3.488

4.  Comparison of Methods To Reweight from Classical Molecular Simulations to QM/MM Potentials.

Authors:  Eric C Dybeck; Gerhard König; Bernard R Brooks; Michael R Shirts
Journal:  J Chem Theory Comput       Date:  2016-03-23       Impact factor: 6.006

5.  Toward Determining ATPase Mechanism in ABC Transporters: Development of the Reaction Path-Force Matching QM/MM Method.

Authors:  Y Zhou; P Ojeda-May; M Nagaraju; J Pu
Journal:  Methods Enzymol       Date:  2016-07-01       Impact factor: 1.600

6.  Accurate Prediction of the Hydration Free Energies of 20 Salts through Adaptive Force Matching and the Proper Comparison with Experimental References.

Authors:  Jicun Li; Feng Wang
Journal:  J Phys Chem B       Date:  2017-06-29       Impact factor: 2.991

7.  Alchemical Binding Free Energy Calculations in AMBER20: Advances and Best Practices for Drug Discovery.

Authors:  Tai-Sung Lee; Bryce K Allen; Timothy J Giese; Zhenyu Guo; Pengfei Li; Charles Lin; T Dwight McGee; David A Pearlman; Brian K Radak; Yujun Tao; Hsu-Chun Tsai; Huafeng Xu; Woody Sherman; Darrin M York
Journal:  J Chem Inf Model       Date:  2020-09-16       Impact factor: 4.956

8.  Signatures of a liquid-liquid transition in an ab initio deep neural network model for water.

Authors:  Thomas E Gartner; Linfeng Zhang; Pablo M Piaggi; Roberto Car; Athanassios Z Panagiotopoulos; Pablo G Debenedetti
Journal:  Proc Natl Acad Sci U S A       Date:  2020-10-02       Impact factor: 11.205

9.  Revised Parameters for the AMOEBA Polarizable Atomic Multipole Water Model.

Authors:  Marie L Laury; Lee-Ping Wang; Vijay S Pande; Teresa Head-Gordon; Jay W Ponder
Journal:  J Phys Chem B       Date:  2015-02-26       Impact factor: 2.991

10.  Toward polarizable AMOEBA thermodynamics at fixed charge efficiency using a dual force field approach: application to organic crystals.

Authors:  Ian J Nessler; Jacob M Litman; Michael J Schnieders
Journal:  Phys Chem Chem Phys       Date:  2016-11-09       Impact factor: 3.676

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