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Mode specific THz spectra of solvated amino acids using the AMOEBA polarizable force field

Alexander Esser, Saurabh Belsare, Dominik Marx, Teresa Head-Gordon
2017 Physical Chemistry, Chemical Physics - PCCP  
We have used the AMOEBA model to simulate the THz spectra of two zwitterionic amino acids in aqueous solution, which is compared to the results on these same systems using ab initio molecular dynamics  ...  Thus a new set of non-bonded parameters of the glycine and valine solutes were required for compatibility with the AMOEBA14 water model.  ...  It originates from polarization effects since fixed charge force fields do not exhibit this cross-correlation signal.  ... 
doi:10.1039/c6cp07388c pmid:28165073 fatcat:as4edj232faopij6gkehtda7te

Polarizable Atomic Multipole-Based Molecular Mechanics for Organic Molecules

Pengyu Ren, Chuanjie Wu, Jay W. Ponder
2011 Journal of Chemical Theory and Computation  
The results obtained in this study suggest that the AMOEBA force field performs well across different environments and phases.  ...  The force field is also used to compute the solvation free energy of 27 compounds not included in the parametrization process, with a RMS error of 0.69 kcal/mol.  ...  calculations and the fixed partial atomic charge based OPLS AA force field.  ... 
doi:10.1021/ct200304d pmid:22022236 pmcid:PMC3196664 fatcat:gztqd7jkm5f43mvsht5zo26jmu

Six-site polarizable model of water based on the classical Drude oscillator

Wenbo Yu, Pedro E. M. Lopes, Benoît Roux, Alexander D. MacKerell
2013 Journal of Chemical Physics  
Overall, improved balance between the description of monomer, dimer, clustered, and bulk phase water is obtained with the new model compared to its SWM4-NDP polarizable predecessor, though application  ...  In addition, comparison of the liquid properties of the SWM6 model is made with those of a number of widely used additive and polarizable models.  ...  Edward Harder for their assistance and for helpful discussions.  ... 
doi:10.1063/1.4774577 pmid:23343286 pmcid:PMC3562330 fatcat:7smwp3rqr5g65mzifvghuc7h6i

Systematic Improvement of a Classical Molecular Model of Water

Lee-Ping Wang, Teresa Head-Gordon, Jay W. Ponder, Pengyu Ren, John D. Chodera, Peter K. Eastman, Todd J. Martinez, Vijay S. Pande
2013 Journal of Physical Chemistry B  
We report the iAMOEBA ("inexpensive AMOEBA") classical polarizable water model.  ...  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  ...  For example, some of the most widely used biomolecular force fieldsincluding the popular AMBER 30−33 and CHARMM models 13,34 are based on the three-site, pairwise-additive TIP3P water model 35 developed  ... 
doi:10.1021/jp403802c pmid:23750713 pmcid:PMC3770532 fatcat:o6jsymzmdjewfalpl5rxuyjqli

TINKTEP: A fully self-consistent, mutually polarizable QM/MM approach based on the AMOEBA force field

Jacek Dziedzic, Yuezhi Mao, Yihan Shao, Jay Ponder, Teresa Head-Gordon, Martin Head-Gordon, Chris-Kriton Skylaris
2016 Journal of Chemical Physics  
The MM subsystem is described by the multipolar, polarizable force field AMOEBA, as implemented in tinker.  ...  1 We present a novel QM/MM approach in which a quantum subsystem is coupled to a classical subsystem described by the AMOEBA polarizable force field.  ...  I Comparison of accuracy offered by fixed point charge (GAFF) and multipolar polarizable (AMOEBA) force-fields in MM calculations and QM/MM calculations.  ... 
doi:10.1063/1.4962909 pmid:27782640 fatcat:r7hqxawwtzgthltn6tfuramq3m

Calculations of the Electric Fields in Liquid Solutions

Stephen D. Fried, Lee-Ping Wang, Steven G. Boxer, Pengyu Ren, Vijay S. Pande
2013 Journal of Physical Chemistry B  
the AMOEBA polarizable force field.  ...  Compared to fixed-charge and continuum models, AMOEBA was the only model examined that could describe nonpolar, polar, and hydrogen bonding environments in a consistent fashion.  ...  The three models employed (Poisson−Boltzmann, fixed-charge force field, AMOEBA force field) qualitatively agree it is on the order of 10−100 MV/cm, and that the change in field between a polar and nonpolar  ... 
doi:10.1021/jp410720y pmid:24304155 pmcid:PMC4211882 fatcat:h3562556l5blpemtcwaqpguyxu

Development of an Advanced Force Field for Water using Variational Energy Decomposition Analysis [article]

A. K. Das, L. Urban, I. Leven, M. Loipersberger, A. Aldossary, M. Head-Gordon, T. Head-Gordon
2019 arXiv   pre-print
analysis, including charge transfer, with force field design choices that reduce the computational expense of the MB-UCB potential while remaining accurate.  ...  Furthermore, by neglecting certain types of molecular interactions such as charge penetration and charge transfer, most classical force fields must rely on, but do not always demonstrate, how cancellation  ...  Lee-Ping Wang for providing all the MD extracted water cluster geometries and corresponding MP2 water binding energies.  ... 
arXiv:1905.07816v3 fatcat:q7rlvu37gfbszgzgscynacmwcq

Molecular modeling and dynamics studies with explicit inclusion of electronic polarizability: theory and applications

Pedro E. M. Lopes, Benoit Roux, Alexander D. MacKerell
2009 Theoretical Chemistry accounts  
Emphasis is placed on water models, for which numerous examples exist, with a more thorough discussion presented on the recently published models associated with the Drudebased CHARMM and the AMOEBA force  ...  Models presented include induced point-dipoles, classical Drude oscillators, and fluctuating charge methods.  ...  Acknowledgments Financial support from the NIH (GM 51501 to A.D.M. and GM 072558 to B.R. and A.D.M.) is acknowledged. BIBLIOGRAPHY  ... 
doi:10.1007/s00214-009-0617-x pmid:20577578 pmcid:PMC2888514 fatcat:3jbvi2fanbghnmdojhayj6qtye

Polarizable Multipolar Molecular Dynamics Using Distributed Point Charges [article]

Mike Devereux, Marco Pezzella, Shampa Raghunathan, Markus Meuwly
2020 arXiv   pre-print
generic point charge alternative to a multipolar electrostatic model for force field development and multilevel simulations.  ...  (M)DCM equivalents for a range of widely used water force fields and for fluorobenzene (PhF) are developed and applied along with the original models to evaluate the impact of reformulating the electrostatic  ...  ACKNOWLEDGEMENT The authors acknowledge financial support from the Swiss National Foundation for Research for their support within the NCCR MUST program and project 200021-117810.  ... 
arXiv:2008.12042v2 fatcat:omsy3tkqkjgpbimspvrzfehyky

Simulating Monovalent and Divalent Ions in Aqueous Solution Using a Drude Polarizable Force Field

Haibo Yu, Troy W. Whitfield, Edward Harder, Guillaume Lamoureux, Igor Vorobyov, Victor M. Anisimov, Alexander D. MacKerell, Benoît Roux
2010 Journal of Chemical Theory and Computation  
The models are parameterized, in conjunction with the polarizable SWM4-NDP water model [Lamoureux et al., Chem. Phys.  ...  Lett. 418, 245 (2006)], to be consistent with a wide assortment of experimentally measured aqueous bulk thermodynamic properties and the energetics of small ion-water clusters.  ...  H.Y. is supported by a postdoctoral fellowship from the Joint Theory Institute of the University of Chicago and Argonne Laboratory. This work was in part funded by NIH grants GM072558 and GM051501.  ... 
doi:10.1021/ct900576a pmid:20300554 pmcid:PMC2838399 fatcat:exzqdc5uprejnfzggrumihotwu

Force Fields for Protein Simulations [chapter]

Jay W. Ponder, David A. Case
2003 Advances in Protein Chemistry  
Alan Grossfield for the WHAM calculations presented in Fig. 5 and Table III and Dr. Pengyu Ren for the AMOEBA polarizable force field results reported in Table IV and Figs. 6 and 7.  ...  Acknowledgments This work was supported by NIH grant GM56531 (to DAC) and NSF grant 9808317 (to JWP). We thank Dr.  ...  The AMOEBA water model (Ren and Ponder, 2003) also gives excellent cluster and liquid phase results and has been designed for compatibility with a protein force field built around a polarizable atomic  ... 
doi:10.1016/s0065-3233(03)66002-x pmid:14631816 fatcat:imkjtojfs5gtrpyqvvu4qzakzi

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

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
2017 Journal of Chemical Theory and Computation  
In terms of the external perturbation, the polMM force field models fall into three general categories.  ...  In practice, molecular and macromolecular simulations using polMM force fields mostly employ ID and DO models.  ...  • The water solvent molecules are treated using a fixed-charge TIP3P model.  ... 
doi:10.1021/acs.jctc.6b01125 pmid:28081366 pmcid:PMC5315702 fatcat:zlopko2iezcgdosmc6ij6liu6y

High-Resolution Mining of SARS-CoV-2 Main Protease Conformational Space: Supercomputer-Driven Unsupervised Adaptive Sampling

Theo Jaffrelot-Inizan, Frédéric CELERSE, Olivier Adjoua, Dina El Ahdab, Luc-Henri Jolly, Chengwen Liu, Pengyu Ren, Matthieu Montes, Nathalie Lagarde, Louis Lagardère, Pierre Monmarché, Jean-Philip Piquemal
2021 Chemical Science  
We provide an unsupervised adaptive sampling strategy capable of producing μs-timescale molecular dynamics (MD) simulations of large biosystems using many-body polarizable force fields (PFF).  ...  Welch Foundation (F-1691) and National Institutes of Health (R01GM106137 and R01GM114237).  ...  FC acknowledges funding from the French state funds managed by the CalSimLab LABEX and the ANR within the Investissements d'Avenir program (reference ANR11-IDEX-0004-02) and support from the Direction  ... 
doi:10.1039/d1sc00145k pmid:34168762 pmcid:PMC8179654 fatcat:vncdghy3bzamzestd7zmrl52ey

Metal Ion Modeling Using Classical Mechanics

Pengfei Li, Kenneth M. Merz
2017 Chemical Reviews  
This Review focuses on classical metal ion modeling based on unpolarized models (including the nonbonded, bonded, cationic dummy atom, and combined models), polarizable models (e.g., the fluctuating charge  ...  Metal ions play significant roles in numerous fields including chemistry, geochemistry, biochemistry, and materials science.  ...  which are compatible with their MB-pol water model.  ... 
doi:10.1021/acs.chemrev.6b00440 pmid:28045509 pmcid:PMC5312828 fatcat:vrfsaiek6bhlbc7rcvsaxteuga

Molecular Dynamics Simulations of Ionic Liquids and Electrolytes Using Polarizable Force Fields

Dmitry Bedrov, Jean-Philip Piquemal, Oleg Borodin, Alexander D. MacKerell, Benoît Roux, Christian Schröder
2019 Chemical Reviews  
Strategies for the development of polarizable models are presented with a specific focus on extracting atomic polarizabilities.  ...  In this manuscript, we review the pros and cons of different treatments of polarization ranging from the mean-field approaches to the most popular explicit polarization models in molecular dynamics simulations  ...  For example, water models progressed from simple three site to 4, 5, and 6 sites and/or multipoles, 210 or Gaussian screened charges 211 in order to improve the description of the electrostatic potential  ... 
doi:10.1021/acs.chemrev.8b00763 pmid:31141351 pmcid:PMC6620131 fatcat:tvkb4yb6ancjllzuckkbwc4xtm
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