Computationally Efficient Multiconfigurational Reactive Molecular Dynamics.
暂无分享,去创建一个
Yuxing Peng | Gregory A. Voth | Takefumi Yamashita | Chris Knight | G. Voth | Christopher Knight | Takefumi Yamashita | Yuxing Peng
[1] Gregory A Voth,et al. Infrared Spectrum of the Hydrated Proton in Water. , 2011, The journal of physical chemistry letters.
[2] Arieh Warshel,et al. Progress in ab initio QM/MM free-energy simulations of electrostatic energies in proteins: accelerated QM/MM studies of pKa, redox reactions and solvation free energies. , 2009, The journal of physical chemistry. B.
[3] Gregory A. Voth,et al. Insights into the mechanism of proton transport in cytochrome c oxidase. , 2012, Journal of the American Chemical Society.
[4] G. Voth,et al. Structure and dynamics of concentrated hydrochloric acid solutions. , 2010, The journal of physical chemistry. B.
[5] Gregory A Voth,et al. A linear-scaling self-consistent generalization of the multistate empirical valence bond method for multiple excess protons in aqueous systems. , 2005, The Journal of chemical physics.
[6] G. Voth,et al. Proton solvation and transport in hydrated nafion. , 2011, The journal of physical chemistry. B.
[7] D. Truhlar,et al. QM/MM: what have we learned, where are we, and where do we go from here? , 2007 .
[8] B. Brooks,et al. Effect of Electrostatic Force Truncation on Interfacial and Transport Properties of Water , 1996 .
[9] F. Paesani,et al. A refined MS-EVB model for proton transport in aqueous environments. , 2012, The journal of physical chemistry. B.
[10] Ivan S. Ufimtsev,et al. A multistate empirical valence bond model for solvation and transport simulations of OH- in aqueous solutions. , 2009, Physical chemistry chemical physics : PCCP.
[11] Gregory A Voth,et al. Molecular dynamics simulation of proton transport near the surface of a phospholipid membrane. , 2002, Biophysical journal.
[12] G. Voth,et al. Coarse-graining in interaction space: a systematic approach for replacing long-range electrostatics with short-range potentials. , 2008, The journal of physical chemistry. B.
[13] P. Brzezinski,et al. The membrane modulates internal proton transfer in cytochrome c oxidase. , 2012, Biochemistry.
[14] Noam Bernstein,et al. QM/MM simulation of liquid water with an adaptive quantum region. , 2012, Physical chemistry chemical physics : PCCP.
[15] J. D. Gezelter,et al. Is the Ewald summation still necessary? Pairwise alternatives to the accepted standard for long-range electrostatics. , 2006, The Journal of chemical physics.
[16] Matt K. Petersen,et al. Characterization of the solvation and transport of the hydrated proton in the perfluorosulfonic acid membrane nafion. , 2006, The journal of physical chemistry. B.
[17] G. Voth,et al. Properties of hydrated excess protons near phospholipid bilayers. , 2010, The journal of physical chemistry. B.
[18] G. Voth,et al. Kinetics of proton migration in liquid water. , 2010, The journal of physical chemistry. B.
[19] Gregory A Voth,et al. A multistate empirical valence bond description of protonatable amino acids. , 2006, The journal of physical chemistry. A.
[20] H. G. Petersen,et al. An algorithm for the simulation of condensed matter which grows as the 3/2 power of the number of particles , 1988 .
[21] D. Thompson,et al. A theoretical study of cis–trans isomerization in HONO using an empirical valence bond potential , 2003 .
[22] J. Alejandre,et al. The Wolf method applied to the liquid-vapor interface of water. , 2008, The Journal of chemical physics.
[23] C. Wick,et al. Investigating hydroxide anion interfacial activity by classical and multistate empirical valence bond molecular dynamics simulations. , 2009, The journal of physical chemistry. A.
[24] G. Voth,et al. Unusual "amphiphilic" association of hydrated protons in strong acid solution. , 2008, Journal of the American Chemical Society.
[25] Gregory A Voth,et al. Defining Condensed Phase Reactive Force Fields from ab Initio Molecular Dynamics Simulations: The Case of the Hydrated Excess Proton. , 2010, Journal of chemical theory and computation.
[26] A. V. Duin,et al. ReaxFF: A Reactive Force Field for Hydrocarbons , 2001 .
[27] D. Clapham,et al. An aqueous H+ permeation pathway in the voltage-gated proton channel Hv1 , 2010, Nature Structural &Molecular Biology.
[28] B. Roux. The calculation of the potential of mean force using computer simulations , 1995 .
[29] D. Laria,et al. Excess protons in water-acetone mixtures. , 2012, The Journal of chemical physics.
[30] Steve Plimpton,et al. Fast parallel algorithms for short-range molecular dynamics , 1993 .
[31] Jessica M J Swanson,et al. Proton solvation and transport in aqueous and biomolecular systems: insights from computer simulations. , 2007, The journal of physical chemistry. B.
[32] Klaus Schulten,et al. Charge delocalization in proton channels, I: the aquaporin channels and proton blockage. , 2007, Biophysical journal.
[33] Shankar Kumar,et al. Multidimensional free‐energy calculations using the weighted histogram analysis method , 1995, J. Comput. Chem..
[34] I. Benjamin,et al. A Molecular Dynamics−Empirical Valence Bond Study of an SN2 Reaction at the Water/Chloroform Interface , 2010 .
[35] Miguel Fuentes-Cabrera,et al. An Evaluation of Molecular Dynamics Performance on the Hybrid Cray XK6 Supercomputer , 2012, ICCS.
[36] Gregory A Voth,et al. Special pair dance and partner selection: elementary steps in proton transport in liquid water. , 2008, The journal of physical chemistry. B.
[37] Thomas Frauenheim,et al. Atomistic simulations of complex materials: ground-state and excited-state properties , 2002 .
[38] Gregory A Voth,et al. Computer simulation of proton solvation and transport in aqueous and biomolecular systems. , 2006, Accounts of chemical research.
[39] Arieh Warshel,et al. An empirical valence bond approach for comparing reactions in solutions and in enzymes , 1980 .
[40] David E. Manolopoulos,et al. A refined ring polymer contraction scheme for systems with electrostatic interactions , 2008 .
[41] Carsten Kutzner,et al. GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation. , 2008, Journal of chemical theory and computation.
[42] C. Wick. Hydronium Behavior at the Air–Water Interface with a Polarizable Multistate Empirical Valence Bond Model , 2012 .
[43] Gregory A Voth,et al. Enhancement of proton conductance by mutations of the selectivity filter of aquaporin-1. , 2011, Journal of molecular biology.
[44] Walter Thiel,et al. QM/MM methods for biomolecular systems. , 2009, Angewandte Chemie.
[45] G. Voth,et al. Origins of proton transport behavior from selectivity domain mutations of the aquaporin-1 channel. , 2006, Biophysical journal.
[46] Gregory A. Voth,et al. The computer simulation of proton transport in water , 1999 .
[47] Gregory A. Voth,et al. The hydrated proton at the water liquid/vapor interface , 2004 .
[48] Barbara Kirchner,et al. Real-world predictions from ab initio molecular dynamics simulations. , 2012, Topics in current chemistry.
[49] D. Manolopoulos,et al. An efficient ring polymer contraction scheme for imaginary time path integral simulations. , 2008, The Journal of chemical physics.
[50] Gregory A Voth,et al. Multiscale reactive molecular dynamics. , 2012, The Journal of chemical physics.
[51] G. Voth,et al. Protons may leak through pure lipid bilayers via a concerted mechanism. , 2005, Biophysical journal.
[52] T. Darden,et al. Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems , 1993 .
[53] Gregory A Voth,et al. Proton transport behavior through the influenza A M2 channel: insights from molecular simulation. , 2007, Biophysical journal.
[54] A. Gil-Villegas,et al. Computer simulation of sedimentation of ionic systems using the Wolf method. , 2012, The Journal of chemical physics.
[55] Gregory A Voth,et al. The curious case of the hydrated proton. , 2012, Accounts of chemical research.
[56] Gregory A Voth,et al. Hydrated excess proton at water-hydrophobic interfaces. , 2009, The journal of physical chemistry. B.
[57] Donald G Truhlar,et al. Electrostatically Embedded Multiconfiguration Molecular Mechanics Based on the Combined Density Functional and Molecular Mechanical Method. , 2008, Journal of chemical theory and computation.