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Rackers JA, Wang Z, Lu C, Laury ML, Lagardère L, Schnieders MJ, Piquemal JP, Ren P, Ponder JW. Tinker 8: Software Tools for Molecular Design. J Chem Theory Comput 2018; 14:5273-5289. [PMID: 30176213 PMCID: PMC6335969 DOI: 10.1021/acs.jctc.8b00529] [Citation(s) in RCA: 290] [Impact Index Per Article: 48.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The Tinker software, currently released as version 8, is a modular molecular mechanics and dynamics package written primarily in a standard, easily portable dialect of Fortran 95 with OpenMP extensions. It supports a wide variety of force fields, including polarizable models such as the Atomic Multipole Optimized Energetics for Biomolecular Applications (AMOEBA) force field. The package runs on Linux, macOS, and Windows systems. In addition to canonical Tinker, there are branches, Tinker-HP and Tinker-OpenMM, designed for use on message passing interface (MPI) parallel distributed memory supercomputers and state-of-the-art graphical processing units (GPUs), respectively. The Tinker suite also includes a tightly integrated Java-based graphical user interface called Force Field Explorer (FFE), which provides molecular visualization capabilities as well as the ability to launch and control Tinker calculations.
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Affiliation(s)
- Joshua A. Rackers
- Program in Computational & Molecular Biophysics, Washington University School of Medicine, Saint Louis, Missouri 63110, United States
| | - Zhi Wang
- Department of Chemistry, Washington University in Saint Louis, Saint Louis, Missouri 63130, United States
| | - Chao Lu
- Department of Chemistry, Washington University in Saint Louis, Saint Louis, Missouri 63130, United States
| | - Marie L. Laury
- Department of Chemistry, Washington University in Saint Louis, Saint Louis, Missouri 63130, United States
| | - Louis Lagardère
- Laboratoire de Chimie Théorique, Sorbonne Universités, UPMC Paris 06, UMR 7616, case courrier 137, 4 place Jussieu, F-75005, Paris, France
| | - Michael J. Schnieders
- Department of Biomedical Engineering, The University of Iowa, Iowa City, IA 52242, United States
| | - Jean-Philip Piquemal
- Laboratoire de Chimie Théorique, Sorbonne Universités, UPMC Paris 06, UMR 7616, case courrier 137, 4 place Jussieu, F-75005, Paris, France
| | - Pengyu Ren
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Jay W. Ponder
- Program in Computational & Molecular Biophysics, Washington University School of Medicine, Saint Louis, Missouri 63110, United States
- Department of Chemistry, Washington University in Saint Louis, Saint Louis, Missouri 63130, United States
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Soley MB, Markmann A, Batista VS. Classical Optimal Control for Energy Minimization Based On Diffeomorphic Modulation under Observable-Response-Preserving Homotopy. J Chem Theory Comput 2018; 14:3351-3362. [DOI: 10.1021/acs.jctc.8b00124] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Micheline B. Soley
- Department of Chemistry, Yale University, P.O.
Box 208107, New Haven, Connecticut 06520-8107, United States
- Energy Sciences Institute, Yale University, P.O.
Box 27394, West Haven, Connecticut 06516-7394, United States
| | - Andreas Markmann
- Department of Chemistry, Yale University, P.O.
Box 208107, New Haven, Connecticut 06520-8107, United States
- Energy Sciences Institute, Yale University, P.O.
Box 27394, West Haven, Connecticut 06516-7394, United States
| | - Victor S. Batista
- Department of Chemistry, Yale University, P.O.
Box 208107, New Haven, Connecticut 06520-8107, United States
- Energy Sciences Institute, Yale University, P.O.
Box 27394, West Haven, Connecticut 06516-7394, United States
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3
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Shigeta Y, Harada R, Sato R, Kitoh-Nishioka H, Bui TKM, Sato A, Tokiwa T, Kyan A, Ishii Y, Kimatsuka M, Yamasaki S, Kayanuma M, Shoji M. Classical cumulant dynamics for statistical chemical physics. MOLECULAR SIMULATION 2017. [DOI: 10.1080/08927022.2017.1315770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Yasuteru Shigeta
- Center for Computational Sciences, University of Tsukuba, Tsukuba, Japan
| | - Ryuhei Harada
- Center for Computational Sciences, University of Tsukuba, Tsukuba, Japan
| | - Ryuma Sato
- Center for Computational Sciences, University of Tsukuba, Tsukuba, Japan
| | | | - Thi Kieu My Bui
- Center for Computational Sciences, University of Tsukuba, Tsukuba, Japan
| | - Akimasa Sato
- Center for Computational Sciences, University of Tsukuba, Tsukuba, Japan
| | - Takaki Tokiwa
- Center for Computational Sciences, University of Tsukuba, Tsukuba, Japan
| | - Akane Kyan
- Center for Computational Sciences, University of Tsukuba, Tsukuba, Japan
| | - Yuki Ishii
- Center for Computational Sciences, University of Tsukuba, Tsukuba, Japan
| | - Masato Kimatsuka
- Center for Computational Sciences, University of Tsukuba, Tsukuba, Japan
| | - Sotaro Yamasaki
- Center for Computational Sciences, University of Tsukuba, Tsukuba, Japan
| | - Megumi Kayanuma
- Center for Computational Sciences, University of Tsukuba, Tsukuba, Japan
| | - Mitsuo Shoji
- Center for Computational Sciences, University of Tsukuba, Tsukuba, Japan
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Soley M, Markmann A, Batista VS. Steered quantum dynamics for energy minimization. J Phys Chem B 2015; 119:715-27. [PMID: 25122515 DOI: 10.1021/jp5046723] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We introduce a quantum optimal control algorithm for energy minimization that combines the diffeomorphic modulation under observable response preserving homotopy (D-MORPH) gradient and the Broyden Fletcher Goldfarb Shanno (BFGS) iterative scheme for nonlinear optimization. An extended set of controls defining the time-dependent mass, dipole moment, and external perturbational field are optimized to find an effective Hamiltonian that steers the dynamics of the system into the global minimum without getting trapped into local minima. The algorithm is illustrated as applied to energy minimization on rugged surfaces and golf potentials comparable to those previously explored for testing quantum annealing methodologies.
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Affiliation(s)
- Micheline Soley
- Department of Chemistry, Yale University , P.O. Box 208107, New Haven, Connecticut 06520-8107, United States
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Hédin F, Plattner N, Doll JD, Meuwly M. Spatial Averaging: Sampling Enhancement for Exploring Configurational Space of Atomic Clusters and Biomolecules. J Chem Theory Comput 2014; 10:4284-96. [DOI: 10.1021/ct500529w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Florent Hédin
- Department
of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | - Nuria Plattner
- Department
of Mathematics and Computer Science, Freie Universität Berlin, Arnimallee 6, D-14195 Berlin, Germany
| | - J. D. Doll
- Department
of Chemistry, Brown University, Providence, Rhode Island 02912, United States
| | - Markus Meuwly
- Department
of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
- Department
of Chemistry, Brown University, Providence, Rhode Island 02912, United States
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7
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Wu X, Cai W, Shao X. A dynamic lattice searching method with rotation operation for optimization of large clusters. Chem Phys 2009. [DOI: 10.1016/j.chemphys.2009.08.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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8
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Zhang C, Ma J. Simulation via direct computation of partition functions. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2007; 76:036708. [PMID: 17930362 PMCID: PMC3133746 DOI: 10.1103/physreve.76.036708] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2007] [Indexed: 05/15/2023]
Abstract
In this paper, we demonstrate the efficiency of simulations via direct computation of the partition function under various macroscopic conditions, such as different temperatures or volumes. The method can compute partition functions by flattening histograms, through, for example, the Wang-Landau recursive scheme, outside the energy space. This method offers a more general and flexible framework for handling various types of ensembles, especially ones in which computation of the density of states is not convenient. It can be easily scaled to large systems, and it is flexible in incorporating Monte Carlo cluster algorithms or molecular dynamics. High efficiency is shown in simulating large Ising models, in finding ground states of simple protein models, and in studying the liquid-vapor phase transition of a simple fluid. The method is very simple to implement and we expect it to be efficient in studying complex systems with rugged energy landscapes, e.g., biological macromolecules.
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Affiliation(s)
- Cheng Zhang
- Department of Bioengineering, Rice University, Houston, Texas 77005, USA
| | - Jianpeng Ma
- Department of Bioengineering, Rice University, Houston, Texas 77005, USA
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, BCM-125, Houston, Texas 77030, USA
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Call ST, Zubarev DY, Boldyrev AI. Global minimum structure searches via particle swarm optimization. J Comput Chem 2007; 28:1177-86. [PMID: 17299774 DOI: 10.1002/jcc.20621] [Citation(s) in RCA: 116] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Novel implementation of the evolutionary approach known as particle swarm optimization (PSO) capable of finding the global minimum of the potential energy surface of atomic assemblies is reported. This is the first time the PSO technique has been used to perform global optimization of minimum structure search for chemical systems. Significant improvements have been introduced to the original PSO algorithm to increase its efficiency and reliability and adapt it to chemical systems. The developed software has successfully found the lowest-energy structures of the LJ(26) Lennard-Jones cluster, anionic silicon hydride Si(2)H(5) (-), and triply hydrated hydroxide ion OH(-) (H(2)O)(3). It requires relatively small population sizes and demonstrates fast convergence. Efficiency of PSO has been compared with simulated annealing, and the gradient embedded genetic algorithm.
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Affiliation(s)
- Seth T Call
- Department of Computer Science, Utah State University, Logan, Utah 84322-0300, USA
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10
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Poulain P, Calvo F, Antoine R, Broyer M, Dugourd P. Performances of Wang-Landau algorithms for continuous systems. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2006; 73:056704. [PMID: 16803071 DOI: 10.1103/physreve.73.056704] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2006] [Indexed: 05/10/2023]
Abstract
The relative performances of different implementations of the Wang-Landau method are assessed on two classes of systems with continuous degrees of freedom, namely, two polypeptides and two atomic Lennard-Jones clusters. Parallel tempering Monte Carlo simulations serve as a reference, and we pay particular attention to the variations of the multiplicative factor f during the course of the simulation. For the systems studied, the Wang-Landau method is found to be of comparable accuracy as parallel tempering, but has significant difficulties in reproducing low-temperature transitions exhibited by the Lennard-Jones clusters at low temperature. Using a complementary order parameter and calculating a two-dimensional joint density of states significantly improves the situation, especially for the notoriously difficult LJ(38) system. However, while parallel tempering easily converges for LJ(31), we have not been able to get data of comparable accuracy with Wang-Landau multicanonical sampling.
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Affiliation(s)
- P Poulain
- Laboratoire de Spectrométrie Ionique et Moléculaire, UMR 5579, Université Lyon I et CNRS, Villeurbanne, France
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11
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Abstract
An alternative exchange strategy for parallel tempering simulations is introduced. Instead of attempting to swap configurations between two randomly chosen but adjacent replicas, the acceptance probabilities of all possible swap moves are calculated a priori. One specific swap move is then selected according to its probability and enforced. The efficiency of the method is illustrated first on the case of two Lennard-Jones (LJ) clusters containing 13 and 31 atoms, respectively. The convergence of the caloric curve is seen to be at least twice as fast as in conventional parallel tempering simulations, especially for the difficult case of LJ31. Further evidence for an improved efficiency is reported on the ergodic measure introduced by Mountain and Thirumalai [J. Phys. Chem. 93, 6975 (1989)], calculated here for LJ13 close to the melting point. Finally, tests on two simple spin systems indicate that the method should be particularly useful when a limited number of replicas are available.
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Affiliation(s)
- F Calvo
- Laboratoire de Physique Quantique, Institut de Recherche sur les Systèmes Atomiques et Moléculaires Complexes (IRSAMC), Université Paul Sabatier, 118 Route de Narbonne, F31062 Toulouse, France.
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12
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Xiang Y, Jiang H, Cai W, Shao X. An Efficient Method Based on Lattice Construction and the Genetic Algorithm for Optimization of Large Lennard-Jones Clusters. J Phys Chem A 2004; 108:3586-3592. [PMID: 28413878 DOI: 10.1021/jp037780t] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yuhong Xiang
- Department of Chemistry, University of Science and Technology of China, Hefei, Anhui, 230026, P. R. China
| | - Haiyan Jiang
- Department of Chemistry, University of Science and Technology of China, Hefei, Anhui, 230026, P. R. China
| | - Wensheng Cai
- Department of Chemistry, University of Science and Technology of China, Hefei, Anhui, 230026, P. R. China
| | - Xueguang Shao
- Department of Chemistry, University of Science and Technology of China, Hefei, Anhui, 230026, P. R. China
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13
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Shao X, Cheng L, Cai W. A dynamic lattice searching method for fast optimization of Lennard-Jones clusters. J Comput Chem 2004; 25:1693-8. [PMID: 15362126 DOI: 10.1002/jcc.20096] [Citation(s) in RCA: 95] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
A highly efficient unbiased global optimization method called dynamic lattice searching (DLS) was proposed. The method starts with a randomly generated local minimum, and finds better solution by a circulation of construction and searching of the dynamic lattice (DL) until the better solution approaches the best solution. The DL is constructed adaptively based on the starting local minimum by searching the possible location sites for an added atom, and the DL searching is implemented by iteratively moving the atom located at the occupied lattice site with the highest energy to the vacant lattice site with the lowest energy. Because the DL can greatly reduce the searching space and the number of the time-consuming local minimization procedures, the proposed DLS method runs at a very high efficiency, especially for the clusters of larger size. The performance of the DLS is investigated in the optimization of Lennard-Jones (LJ) clusters up to 309 atoms, and the structure of the LJ(500) is also predicted. Furthermore, the idea of dynamic lattice can be easily adopted in the optimization of other molecular or atomic clusters. It may be a promising approach to be universally used for structural optimizations in the chemistry field.
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Affiliation(s)
- Xueguang Shao
- Department of Chemistry, University of Science and Technology of China, Hefei, Anhui 230026, People's Republic of China.
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Abstract
Predicting protein structures from their amino acid sequences is a problem of global optimization. Global optima (native structures) are often sought using stochastic sampling methods such as Monte Carlo or molecular dynamics, but these methods are slow. In contrast, there are fast deterministic methods that find near-optimal solutions of well-known global optimization problems such as the traveling salesman problem (TSP). But fast TSP strategies have yet to be applied to protein folding, because of fundamental differences in the two types of problems. Here, we show how protein folding can be framed in terms of the TSP, to which we apply a variation of the Durbin-Willshaw elastic net optimization strategy. We illustrate using a simple model of proteins with database-derived statistical potentials and predicted secondary structure restraints. This optimization strategy can be applied to many different models and potential functions, and can readily incorporate experimental restraint information. It is also fast; with the simple model used here, the method finds structures that are within 5-6 A all-Calpha-atom RMSD of the known native structures for 40-mers in about 8 s on a PC; 100-mers take about 20 s. The computer time tau scales as tau approximately n, where n is the number of amino acids. This method may prove to be useful for structure refinement and prediction.
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Affiliation(s)
- Keith D Ball
- Department of Pharmaceutical Chemistry, University of California at San Francisco, 94118, USA.
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15
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Lee YH, Berne BJ. Quantum Thermal Annealing with Renormalization: Application to a Frustrated Model Protein. J Phys Chem A 2000. [DOI: 10.1021/jp002589u] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yong-Han Lee
- Department of Chemistry and Center for Biomolecular Simulation, Columbia University, 3000 Broadway, New York, New York 10027
| | - B. J. Berne
- Department of Chemistry and Center for Biomolecular Simulation, Columbia University, 3000 Broadway, New York, New York 10027
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18
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Lee YH, Berne BJ. Global Optimization: Quantum Thermal Annealing with Path Integral Monte Carlo. J Phys Chem A 1999. [DOI: 10.1021/jp991868i] [Citation(s) in RCA: 65] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Yong-Han Lee
- Department of Chemistry and Center for Biomolecular Simulation, Columbia University, 3000 Broadway, New York, New York 10027
| | - B. J. Berne
- Department of Chemistry and Center for Biomolecular Simulation, Columbia University, 3000 Broadway, New York, New York 10027
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Starikov EB, Lehrach H, Wanker EE. Folding of oligoglutamines: a theoretical approach based upon thermodynamics and molecular mechanics. J Biomol Struct Dyn 1999; 17:409-27. [PMID: 10636078 DOI: 10.1080/07391102.1999.10508374] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Folding of oligoglutamine chains of different lengths is of crucial interest for exploring the molecular mechanisms of Huntington's disease. A simple oligoglutamine model based upon the Flory-Huggins theory of polymer solutions demonstrates a random coil instability in chains containing more than 40 glutamine residues with respect to beta-sheet formation. This is in striking quantitative agreement with biochemical results on the chain length dependence of polyglutamine aggregation in vivo and in vitro, as well as with clinical data on the polyglutamine chain length dependence of the onset of Huntington's disease. Furthermore, a detailed molecular-mechanical investigation of a polypeptide chain carrying 40 glutamine residues was performed. Two possible folding modes of such an oligoglutamine chain were revealed: a) a beta-hairpin and b) a highly compact random coil entity stabilized by a wealth of H-bonds among the glutamine side chains. A possible role of these folding modes in polyglutamine aggregation, as well as in the onset of Huntington's disease, is discussed.
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Affiliation(s)
- E B Starikov
- Institute for Crystallography, Free University of Berlin, Germany.
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21
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Pillardy J, Liwo A, Scheraga HA. An Efficient Deformation-Based Global Optimization Method (Self-Consistent Basin-to-Deformed-Basin Mapping (SCBDBM)). Application to Lennard-Jones Atomic Clusters. J Phys Chem A 1999. [DOI: 10.1021/jp992741w] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jarosław Pillardy
- Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853-1301, and Department of Chemistry, University of Gdańsk, ul. Sobieskiego 18, 80-952 Gdańsk, Poland
| | - Adam Liwo
- Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853-1301, and Department of Chemistry, University of Gdańsk, ul. Sobieskiego 18, 80-952 Gdańsk, Poland
| | - Harold A. Scheraga
- Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853-1301, and Department of Chemistry, University of Gdańsk, ul. Sobieskiego 18, 80-952 Gdańsk, Poland
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Abstract
Finding the optimal solution to a complex optimization problem is of great importance in many fields, ranging from protein structure prediction to the design of microprocessor circuitry. Some recent progress in finding the global minima of potential energy functions is described, focusing on applications of the simple "basin-hopping" approach to atomic and molecular clusters and more complicated hypersurface deformation techniques for crystals and biomolecules. These methods have produced promising results and should enable larger and more complex systems to be treated in the future.
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Affiliation(s)
- D J Wales
- University Chemical Laboratories, Lensfield Road, Cambridge, CB2 1EW, UK.
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23
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Pappu RV, Hart RK, Ponder JW. Analysis and Application of Potential Energy Smoothing and Search Methods for Global Optimization. J Phys Chem B 1998. [DOI: 10.1021/jp982255t] [Citation(s) in RCA: 218] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Rohit V. Pappu
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110
| | - Reece K. Hart
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110
| | - Jay W. Ponder
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110
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25
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Klein CT, Mayer B, K�hler G, Wolschann P. Systematic stepsize variation: Efficient method for searching conformational space of polypeptides. J Comput Chem 1998. [DOI: 10.1002/(sici)1096-987x(199810)19:13<1470::aid-jcc4>3.0.co;2-n] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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26
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Pillardy J, Piela L. Smoothing techniques of global optimization: Distance scaling method in searches for most stable Lennard-Jones atomic clusters. J Comput Chem 1997. [DOI: 10.1002/(sici)1096-987x(199712)18:16<2040::aid-jcc8>3.0.co;2-l] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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27
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Wales DJ, Doye JPK. Global Optimization by Basin-Hopping and the Lowest Energy Structures of Lennard-Jones Clusters Containing up to 110 Atoms. J Phys Chem A 1997. [DOI: 10.1021/jp970984n] [Citation(s) in RCA: 2261] [Impact Index Per Article: 83.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- David J. Wales
- University Chemical Laboratories, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Jonathan P. K. Doye
- FOM Institute for Atomic and Molecular Physics, Kruislaan 407, 1098 SJ Amsterdam, The Netherlands
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28
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Serra P, Stanton AF, Kais S, Bleil RE. Comparison study of pivot methods for global optimization. J Chem Phys 1997. [DOI: 10.1063/1.473678] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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29
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Schelstraete S, Verschelde H. Finding Minimum-Energy Configurations of Lennard-Jones Clusters Using an Effective Potential. J Phys Chem A 1997. [DOI: 10.1021/jp9621181] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Sigurd Schelstraete
- University of Gent, Department of mathematical Physics and Astronomy, Krijgslaan 281-S9, B-9000 Gent, Belgium
| | - Henri Verschelde
- University of Gent, Department of mathematical Physics and Astronomy, Krijgslaan 281-S9, B-9000 Gent, Belgium
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30
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31
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Doye JPK, Wales DJ. On potential energy surfaces and relaxation to the global minimum. J Chem Phys 1996. [DOI: 10.1063/1.472697] [Citation(s) in RCA: 81] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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32
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Amara P, Straub JE. Energy minimization using the classical density distribution: Application to sodium chloride clusters. PHYSICAL REVIEW. B, CONDENSED MATTER 1996; 53:13857-13863. [PMID: 9983141 DOI: 10.1103/physrevb.53.13857] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
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33
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Ma J, Straub JE. Erratum: Simulated annealing using the classical density distribution [J. Chem. Phys. 101, 533 (1994)]. J Chem Phys 1995. [DOI: 10.1063/1.470733] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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34
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Field MJ. Global optimization usingab initioquantum mechanical potentials and simulated annealing of the classical Liouville equation. J Chem Phys 1995. [DOI: 10.1063/1.470064] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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35
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Ma J, Straub JE, Shakhnovich EI. Simulation study of the collapse of linear and ring homopolymers. J Chem Phys 1995. [DOI: 10.1063/1.470522] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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36
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Straub JE, Ma J, Amara P. Simulated annealing using coarse grained classical dynamics: Smoluchowski dynamics in the Gaussian density approximation. J Chem Phys 1995. [DOI: 10.1063/1.469779] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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