GOMC: GPU Optimized Monte Carlo for the simulation of phase equilibria and physical properties of complex fluids
暂无分享,去创建一个
Loren Schwiebert | Kamel Rushaidat | Jason R. Mick | Jeffrey J. Potoff | Yuanzhe Li | Brock Jackman | Younes Nejahi | Mohammad Soroush Barhaghi | L. Schwiebert | J. Potoff | M. S. Barhaghi | J. Mick | Younes Nejahi | B. Jackman | Kamel Rushaidat | Yuanzhe Li
[1] K Schulten,et al. Reconstructing potential energy functions from simulated force-induced unbinding processes. , 1997, Biophysical journal.
[2] Ross C. Walker,et al. An overview of the Amber biomolecular simulation package , 2013 .
[3] Michael R. Shirts,et al. Dynamical reweighting: improved estimates of dynamical properties from simulations at multiple temperatures. , 2011, The Journal of chemical physics.
[4] Ganesh Kamath,et al. Transferable potentials for phase equilibria. 8. United-atom description for thiols, sulfides, disulfides, and thiophene. , 2005, The journal of physical chemistry. B.
[5] Jay W Ponder,et al. Revised Parameters for the AMOEBA Polarizable Atomic Multipole Water Model. , 2015, The journal of physical chemistry. B.
[6] Klaus Schulten,et al. High-performance scalable molecular dynamics simulations of a polarizable force field based on classical Drude oscillators in NAMD. , 2011, The journal of physical chemistry letters.
[7] David S. Sholl,et al. Progress, Opportunities, and Challenges for Applying Atomically Detailed Modeling to Molecular Adsorption and Transport in Metal−Organic Framework Materials , 2009 .
[8] J. Ilja Siepmann,et al. Monte Carlo algorithms for simulating systems with adiabatic separation of electronic and nuclear degrees of freedom , 1999 .
[9] Sayee Prasaad Balaji,et al. Optimization of Particle Transfers in the Gibbs Ensemble for Systems with Strong and Directional Interactions Using CBMC, CFCMC, and CB/CFCMC , 2016 .
[10] A. Panagiotopoulos. Direct determination of phase coexistence properties of fluids by Monte Carlo simulation in a new ensemble , 1987 .
[11] Wei Shi,et al. Continuous Fractional Component Monte Carlo: An Adaptive Biasing Method for Open System Atomistic Simulations. , 2007, Journal of chemical theory and computation.
[12] Richard Gowers,et al. Automated analysis and benchmarking of GCMC simulation programs in application to gas adsorption , 2018 .
[13] Greg van Anders,et al. Digital Alchemy for Materials Design: Colloids and Beyond. , 2015, ACS nano.
[14] W. L. Jorgensen,et al. Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids , 1996 .
[15] R. Snurr,et al. RASPA: molecular simulation software for adsorption and diffusion in flexible nanoporous materials , 2016 .
[16] Tony Hey,et al. Open science decoded , 2015, Nature Physics.
[17] Georgios C. Boulougouris,et al. Engineering a Molecular Model for Water Phase Equilibrium over a Wide Temperature Range , 1998 .
[18] Benoît Roux,et al. Modeling induced polarization with classical Drude oscillators: Theory and molecular dynamics simulation algorithm , 2003 .
[19] T. Straatsma,et al. THE MISSING TERM IN EFFECTIVE PAIR POTENTIALS , 1987 .
[20] Callum J. Dickson,et al. GAFFlipid: a General Amber Force Field for the accurate molecular dynamics simulation of phospholipid , 2012 .
[21] Alexander D. MacKerell,et al. CHARMM general force field: A force field for drug‐like molecules compatible with the CHARMM all‐atom additive biological force fields , 2009, J. Comput. Chem..
[22] S. L. Mayo,et al. DREIDING: A generic force field for molecular simulations , 1990 .
[23] J. Ilja Siepmann,et al. Transferable Potentials for Phase Equilibria. 6. United-Atom Description for Ethers, Glycols, Ketones, and Aldehydes , 2004 .
[24] Randall Q Snurr,et al. Screening of metal-organic frameworks for carbon dioxide capture from flue gas using a combined experimental and modeling approach. , 2009, Journal of the American Chemical Society.
[25] A. Chaffee,et al. Ewald Summation for Molecular Simulations. , 2015, Journal of chemical theory and computation.
[26] Neeraj Rai,et al. Transferable potentials for phase equilibria. 7. Primary, secondary, and tertiary amines, nitroalkanes and nitrobenzene, nitriles, amides, pyridine, and pyrimidine. , 2005, The journal of physical chemistry. B.
[27] W. L. Jorgensen. The Many Roles of Computation in Drug Discovery , 2004, Science.
[28] J. Potoff,et al. Mie potentials for phase equilibria calculations: application to alkanes and perfluoroalkanes. , 2009, The journal of physical chemistry. B.
[29] Li-Chiang Lin,et al. Mail-Order Metal–Organic Frameworks (MOFs): Designing Isoreticular MOF-5 Analogues Comprising Commercially Available Organic Molecules , 2013 .
[30] J. Potoff,et al. Optimised Mie potentials for phase equilibria: application to alkynes , 2017 .
[31] K. Schulten,et al. Disulfide Bridges: Bringing Together Frustrated Structure in a Bioactive Peptide. , 2016, Biophysical journal.
[32] Peng Wang,et al. Implementing molecular dynamics on hybrid high performance computers - short range forces , 2011, Comput. Phys. Commun..
[33] Maciej Haranczyk,et al. Metal–organic framework with optimally selective xenon adsorption and separation , 2016, Nature Communications.
[34] L. Schwiebert,et al. Optimized Mie Potentials for Phase Equilibria: Application to Branched Alkanes , 2017 .
[35] Joshua A. Anderson,et al. General purpose molecular dynamics simulations fully implemented on graphics processing units , 2008, J. Comput. Phys..
[36] G. Kamath,et al. Mie Potentials for Phase Equilibria: Application to Alkenes , 2014 .
[37] C. Wilmer,et al. Towards rapid computational screening of metal-organic frameworks for carbon dioxide capture: Calculation of framework charges via charge equilibration , 2011 .
[38] Loren Schwiebert,et al. GPU-accelerated Gibbs ensemble Monte Carlo simulations of Lennard-Jonesium , 2013, Comput. Phys. Commun..
[39] Alexander P. Lyubartsev,et al. Derivation and Systematic Validation of a Refined All-Atom Force Field for Phosphatidylcholine Lipids , 2012, The journal of physical chemistry. B.
[40] C. Wilmer,et al. Large-scale screening of hypothetical metal-organic frameworks. , 2012, Nature chemistry.
[41] Alexander D. MacKerell,et al. Balancing the Interactions of Ions, Water, and DNA in the Drude Polarizable Force Field , 2014, The journal of physical chemistry. B.
[42] Jianpeng Ma,et al. CHARMM: The biomolecular simulation program , 2009, J. Comput. Chem..
[43] Jeffery B. Klauda,et al. Simulation-based methods for interpreting x-ray data from lipid bilayers. , 2006, Biophysical journal.
[44] T. Vlugt,et al. Computing the Heat of Adsorption using Molecular Simulations: The Effect of Strong Coulombic Interactions. , 2008, Journal of chemical theory and computation.
[45] Wei Shi,et al. Improvement in molecule exchange efficiency in Gibbs ensemble Monte Carlo: Development and implementation of the continuous fractional component move , 2008, J. Comput. Chem..
[46] S. Glotzer,et al. Anisotropy of building blocks and their assembly into complex structures. , 2007, Nature materials.
[47] Hans Hasse,et al. ms2: A molecular simulation tool for thermodynamic properties, new version release , 2014, Comput. Phys. Commun..
[48] D. Tieleman,et al. The MARTINI force field: coarse grained model for biomolecular simulations. , 2007, The journal of physical chemistry. B.
[49] Berend Smit,et al. Understanding molecular simulation: from algorithms to applications , 1996 .
[50] Michael F. Crowley,et al. New faster CHARMM molecular dynamics engine , 2013, J. Comput. Chem..
[51] Hans Hasse,et al. ms2: A molecular simulation tool for thermodynamic properties , 2011, Comput. Phys. Commun..
[52] Michael Engel,et al. Massively parallel Monte Carlo for many-particle simulations on GPUs , 2012, J. Comput. Phys..
[53] William L Jorgensen,et al. Efficient drug lead discovery and optimization. , 2009, Accounts of chemical research.
[54] Andrew S. Paluch,et al. Cassandra: An open source Monte Carlo package for molecular simulation , 2017, J. Comput. Chem..
[55] Eric F Darve,et al. Calculating free energies using average force , 2001 .
[56] Alexander D. MacKerell,et al. Update of the CHARMM all-atom additive force field for lipids: validation on six lipid types. , 2010, The journal of physical chemistry. B.
[57] Duncan Poole,et al. Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 2. Explicit Solvent Particle Mesh Ewald. , 2013, Journal of chemical theory and computation.
[58] Hans Hasse,et al. ms2: A molecular simulation tool for thermodynamic properties, release 3.0 , 2017, Comput. Phys. Commun..
[59] Steve Plimpton,et al. Fast parallel algorithms for short-range molecular dynamics , 1993 .
[60] Holger Gohlke,et al. The Amber biomolecular simulation programs , 2005, J. Comput. Chem..
[61] David A. Kofke,et al. Etomica: An object‐oriented framework for molecular simulation , 2015, J. Comput. Chem..
[62] K Schulten,et al. VMD: visual molecular dynamics. , 1996, Journal of molecular graphics.
[63] L. Schwiebert,et al. Optimized Mie potentials for phase equilibria: Application to noble gases and their mixtures with n-alkanes. , 2015, The Journal of chemical physics.
[64] J. Ilja Siepmann,et al. Monte Carlo Calculations for Alcohols and Their Mixtures with Alkanes. Transferable Potentials for Phase Equilibria. 5. United-Atom Description of Primary, Secondary, and Tertiary Alcohols , 2001 .
[65] Alan M. Ferrenberg,et al. New Monte Carlo technique for studying phase transitions. , 1988, Physical review letters.
[66] Richard L. Martin,et al. Large-scale computational screening of zeolites for ethane/ethene separation. , 2012, Langmuir : the ACS journal of surfaces and colloids.
[67] J. Ilja Siepmann,et al. Novel Configurational-Bias Monte Carlo Method for Branched Molecules. Transferable Potentials for Phase Equilibria. 2. United-Atom Description of Branched Alkanes , 1999 .
[68] Laxmikant V. Kalé,et al. Scalable molecular dynamics with NAMD , 2005, J. Comput. Chem..
[69] K. Schulten,et al. Physical properties of the HIV-1 capsid from all-atom molecular dynamics simulations , 2017, Nature Communications.
[70] J. Ilja Siepmann,et al. Vapor–liquid equilibria of mixtures containing alkanes, carbon dioxide, and nitrogen , 2001 .
[71] Sharon C. Glotzer,et al. Rigid body constraints realized in massively-parallel molecular dynamics on graphics processing units , 2011, Comput. Phys. Commun..
[72] Junmei Wang,et al. Development and testing of a general amber force field , 2004, J. Comput. Chem..
[73] J. Ilja Siepmann,et al. Transferable Potentials for Phase Equilibria. 1. United-Atom Description of n-Alkanes , 1998 .
[74] S. Glotzer,et al. Self-Assembly of Patchy Particles. , 2004, Nano letters.
[75] Sayee Prasaad Balaji,et al. A Comparison of Advanced Monte Carlo Methods for Open Systems: CFCMC vs CBMC. , 2014, Journal of chemical theory and computation.
[76] M. G. Martin. MCCCS Towhee: a tool for Monte Carlo molecular simulation , 2013 .
[77] J. Ilja Siepmann,et al. Transferable Potentials for Phase Equilibria. 4. United-Atom Description of Linear and Branched Alkenes and Alkylbenzenes , 2000 .
[78] David N. LeBard,et al. Self-assembly of coarse-grained ionic surfactants accelerated by graphics processing units , 2012 .
[79] Alan M. Ferrenberg,et al. Optimized Monte Carlo data analysis. , 1989, Physical Review Letters.
[80] Alexander D. MacKerell,et al. Identification and validation of human DNA ligase inhibitors using computer-aided drug design. , 2008, Journal of medicinal chemistry.
[81] Michael O'Keeffe,et al. Systematic Design of Pore Size and Functionality in Isoreticular MOFs and Their Application in Methane Storage , 2002, Science.
[82] R. Böckmann,et al. Optimization of the OPLS-AA Force Field for Long Hydrocarbons. , 2012, Journal of chemical theory and computation.
[83] Berk Hess,et al. GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers , 2015 .
[84] J. Potoff,et al. Prediction of Radon-222 Phase Behavior by Monte Carlo Simulation , 2016 .