Literature DB >> 23750713

Systematic improvement of a classical molecular model of water.

Lee-Ping Wang1, Teresa Head-Gordon, Jay W Ponder, Pengyu Ren, John D Chodera, Peter K Eastman, Todd J Martinez, Vijay S Pande.   

Abstract

We report the iAMOEBA ("inexpensive AMOEBA") classical polarizable water model. The iAMOEBA model uses a direct approximation to describe electronic polarizability, in which the induced dipoles are determined directly from the permanent multipole electric fields and do not interact with one another. The direct approximation reduces the computational cost relative to a fully self-consistent polarizable model such as AMOEBA. The model is parameterized using ForceBalance, a systematic optimization method that simultaneously utilizes training data from experimental measurements and high-level ab initio calculations. We show that iAMOEBA is a highly accurate model for water in the solid, liquid, and gas phases, with the ability to fully capture the effects of electronic polarization and predict a comprehensive set of water properties beyond the training data set including the phase diagram. The increased accuracy of iAMOEBA over the fully polarizable AMOEBA model demonstrates ForceBalance as a method that allows the researcher to systematically improve empirical models by efficiently utilizing the available data.

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Year:  2013        PMID: 23750713      PMCID: PMC3770532          DOI: 10.1021/jp403802c

Source DB:  PubMed          Journal:  J Phys Chem B        ISSN: 1520-5207            Impact factor:   2.991


  75 in total

1.  Phase-space overlap measures. I. Fail-safe bias detection in free energies calculated by molecular simulation.

Authors:  Di Wu; David A Kofke
Journal:  J Chem Phys       Date:  2005-08-01       Impact factor: 3.488

Review 2.  Advances in methods and algorithms in a modern quantum chemistry program package.

Authors:  Yihan Shao; Laszlo Fusti Molnar; Yousung Jung; Jörg Kussmann; Christian Ochsenfeld; Shawn T Brown; Andrew T B Gilbert; Lyudmila V Slipchenko; Sergey V Levchenko; Darragh P O'Neill; Robert A DiStasio; Rohini C Lochan; Tao Wang; Gregory J O Beran; Nicholas A Besley; John M Herbert; Ching Yeh Lin; Troy Van Voorhis; Siu Hung Chien; Alex Sodt; Ryan P Steele; Vitaly A Rassolov; Paul E Maslen; Prakashan P Korambath; Ross D Adamson; Brian Austin; Jon Baker; Edward F C Byrd; Holger Dachsel; Robert J Doerksen; Andreas Dreuw; Barry D Dunietz; Anthony D Dutoi; Thomas R Furlani; Steven R Gwaltney; Andreas Heyden; So Hirata; Chao-Ping Hsu; Gary Kedziora; Rustam Z Khalliulin; Phil Klunzinger; Aaron M Lee; Michael S Lee; Wanzhen Liang; Itay Lotan; Nikhil Nair; Baron Peters; Emil I Proynov; Piotr A Pieniazek; Young Min Rhee; Jim Ritchie; Edina Rosta; C David Sherrill; Andrew C Simmonett; Joseph E Subotnik; H Lee Woodcock; Weimin Zhang; Alexis T Bell; Arup K Chakraborty; Daniel M Chipman; Frerich J Keil; Arieh Warshel; Warren J Hehre; Henry F Schaefer; Jing Kong; Anna I Krylov; Peter M W Gill; Martin Head-Gordon
Journal:  Phys Chem Chem Phys       Date:  2006-06-12       Impact factor: 3.676

3.  Development of transferable interaction potentials for water. V. Extension of the flexible, polarizable, Thole-type model potential (TTM3-F, v. 3.0) to describe the vibrational spectra of water clusters and liquid water.

Authors:  George S Fanourgakis; Sotiris S Xantheas
Journal:  J Chem Phys       Date:  2008-02-21       Impact factor: 3.488

4.  The relative entropy is fundamental to multiscale and inverse thermodynamic problems.

Authors:  M Scott Shell
Journal:  J Chem Phys       Date:  2008-10-14       Impact factor: 3.488

5.  Communication: The effect of dispersion corrections on the melting temperature of liquid water.

Authors:  Soohaeng Yoo; Sotiris S Xantheas
Journal:  J Chem Phys       Date:  2011-03-28       Impact factor: 3.488

6.  Folding Proteins at 500 ns/hour with Work Queue.

Authors:  Badi' Abdul-Wahid; Li Yu; Dinesh Rajan; Haoyun Feng; Eric Darve; Douglas Thain; Jesús A Izaguirre
Journal:  Proc IEEE Int Conf Escience       Date:  2012-10

7.  Hydrogen bonds in liquid water are broken only fleetingly.

Authors:  J D Eaves; J J Loparo; C J Fecko; S T Roberts; A Tokmakoff; P L Geissler
Journal:  Proc Natl Acad Sci U S A       Date:  2005-08-31       Impact factor: 11.205

8.  Observation of a Zundel-like transition state during proton transfer in aqueous hydroxide solutions.

Authors:  Sean T Roberts; Poul B Petersen; Krupa Ramasesha; Andrei Tokmakoff; Ivan S Ufimtsev; Todd J Martinez
Journal:  Proc Natl Acad Sci U S A       Date:  2009-07-31       Impact factor: 11.205

9.  Optimization of the additive CHARMM all-atom protein force field targeting improved sampling of the backbone φ, ψ and side-chain χ(1) and χ(2) dihedral angles.

Authors:  Robert B Best; Xiao Zhu; Jihyun Shim; Pedro E M Lopes; Jeetain Mittal; Michael Feig; Alexander D Mackerell
Journal:  J Chem Theory Comput       Date:  2012-07-18       Impact factor: 6.006

10.  Improved side-chain torsion potentials for the Amber ff99SB protein force field.

Authors:  Kresten Lindorff-Larsen; Stefano Piana; Kim Palmo; Paul Maragakis; John L Klepeis; Ron O Dror; David E Shaw
Journal:  Proteins       Date:  2010-06
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  71 in total

1.  Toward Learned Chemical Perception of Force Field Typing Rules.

Authors:  Camila Zanette; Caitlin C Bannan; Christopher I Bayly; Josh Fass; Michael K Gilson; Michael R Shirts; John D Chodera; David L Mobley
Journal:  J Chem Theory Comput       Date:  2018-12-24       Impact factor: 6.006

2.  Efficient treatment of induced dipoles.

Authors:  Andrew C Simmonett; Frank C Pickard; Yihan Shao; Thomas E Cheatham; Bernard R Brooks
Journal:  J Chem Phys       Date:  2015-08-21       Impact factor: 3.488

3.  LICHEM: A QM/MM program for simulations with multipolar and polarizable force fields.

Authors:  Eric G Kratz; Alice R Walker; Louis Lagardère; Filippo Lipparini; Jean-Philip Piquemal; G Andrés Cisneros
Journal:  J Comput Chem       Date:  2016-01-18       Impact factor: 3.376

4.  An Estimation of Hybrid Quantum Mechanical Molecular Mechanical Polarization Energies for Small Molecules Using Polarizable Force-Field Approaches.

Authors:  Jing Huang; Ye Mei; Gerhard König; Andrew C Simmonett; Frank C Pickard; Qin Wu; Lee-Ping Wang; Alexander D MacKerell; Bernard R Brooks; Yihan Shao
Journal:  J Chem Theory Comput       Date:  2017-01-24       Impact factor: 6.006

5.  AMOEBA+ Classical Potential for Modeling Molecular Interactions.

Authors:  Chengwen Liu; Jean-Philip Piquemal; Pengyu Ren
Journal:  J Chem Theory Comput       Date:  2019-06-11       Impact factor: 6.006

6.  Water is not a dynamic polydisperse branched polymer.

Authors:  Teresa Head-Gordon; Francesco Paesani
Journal:  Proc Natl Acad Sci U S A       Date:  2019-06-25       Impact factor: 11.205

Review 7.  Biomolecular force fields: where have we been, where are we now, where do we need to go and how do we get there?

Authors:  Pnina Dauber-Osguthorpe; A T Hagler
Journal:  J Comput Aided Mol Des       Date:  2018-11-30       Impact factor: 3.686

8.  Toward Improved Force-Field Accuracy through Sensitivity Analysis of Host-Guest Binding Thermodynamics.

Authors:  Jian Yin; Andrew T Fenley; Niel M Henriksen; Michael K Gilson
Journal:  J Phys Chem B       Date:  2015-08-05       Impact factor: 2.991

9.  Escaping Atom Types in Force Fields Using Direct Chemical Perception.

Authors:  David L Mobley; Caitlin C Bannan; Andrea Rizzi; Christopher I Bayly; John D Chodera; Victoria T Lim; Nathan M Lim; Kyle A Beauchamp; David R Slochower; Michael R Shirts; Michael K Gilson; Peter K Eastman
Journal:  J Chem Theory Comput       Date:  2018-10-30       Impact factor: 6.006

10.  United polarizable multipole water model for molecular mechanics simulation.

Authors:  Rui Qi; Lee-Ping Wang; Qiantao Wang; Vijay S Pande; Pengyu Ren
Journal:  J Chem Phys       Date:  2015-07-07       Impact factor: 3.488

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