Locating critical points on multi-dimensional surfaces by genetic algorithm: test cases including normal and perturbed argon clusters

Abstract It is demonstrated that Genetic Algorithm in a floating point realisation can be a viable tool for locating critical points on a multi-dimensional potential energy surface (PES). For small clusters, the standard algorithm works well. For bigger ones, the search for global minimum becomes more efficient when used in conjunction with coordinate stretching, and partitioning of the strings into a core part and an outer part which are alternately optimized The method works with equal facility for locating minima, local as well as global, and saddle points (SP) of arbitrary orders . The search for minima requires computation of the gradient vector, but not the Hessian, while that for SP's requires the information of the gradient vector and the Hessian, the latter only at some specific points on the path. The method proposed is tested on (i) a model 2-d PES (ii) argon clusters (Ar 4 –Ar 30 ) in which argon atoms interact via Lennard-Jones potential, (iii) Ar m X, m =12 clusters where X may be a neutral atom or a cation. We also explore if the method could also be used to construct what may be called a stochastic representation of the reaction path on a given PES with reference to conformational changes in Ar n clusters.

[1]  S. Peyerimhoff,et al.  Stability and structure of singly-charged xenon-argon clusters [Xe1Arn−1]+,n=3–27 , 1988 .

[2]  M. Zerner,et al.  A survey of optimization procedures for stable structures and transition states , 1988 .

[3]  S. Farantos,et al.  POTENTIAL FUNCTIONS AND STATIC AND DYNAMIC PROPERTIES OF MGM+ARN (M=1,2; N=1-18) CLUSTERS , 1996 .

[4]  Juan C. Meza,et al.  Do intelligent configuration search techniques outperform random search for large molecules , 1992 .

[5]  H. Scheraga,et al.  Performance of the diffusion equation method in searches for optimum structures of clusters of Lennard-Jones atoms , 1991 .

[6]  Howard R. Mayne,et al.  An investigation of two approaches to basin hopping minimization for atomic and molecular clusters , 1998 .

[7]  Wayne J. Pullan,et al.  Structure Prediction of Benzene Clusters Using a Genetic Algorithm , 1997, J. Chem. Inf. Comput. Sci..

[8]  L. Piela,et al.  Molecular Dynamics on Deformed Potential Energy Hypersurfaces , 1995 .

[9]  Ho,et al.  Molecular geometry optimization with a genetic algorithm. , 1995, Physical review letters.

[10]  P. Argos,et al.  Potential of genetic algorithms in protein folding and protein engineering simulations. , 1992, Protein engineering.

[11]  S. Sun,et al.  Reduced representation model of protein structure prediction: Statistical potential and genetic algorithms , 1993, Protein science : a publication of the Protein Society.

[12]  A. Ding,et al.  Fragmentation spectroscopy of heterogeneous clusters , 1988 .

[13]  D. D. Morrison Optimization by Least Squares , 1968 .

[14]  A random walk to local minima and saddle points on a potential energy surface. A strategy based on simulated annealing , 1996 .

[15]  Howard R. Mayne,et al.  Minimization of small silicon clusters using the space-fixed modified genetic algorithm method , 1996 .

[16]  D. Wales Finding saddle points for clusters , 1989 .

[17]  P Argos,et al.  Folding the main chain of small proteins with the genetic algorithm. , 1994, Journal of molecular biology.

[18]  David E. Goldberg,et al.  Genetic Algorithms in Search Optimization and Machine Learning , 1988 .

[19]  Howard R. Mayne,et al.  Global geometry optimization of atomic clusters using a modified genetic algorithm in space‐fixed coordinates , 1996 .

[20]  K. Dill,et al.  A simple protein folding algorithm using a binary code and secondary structure constraints. , 1995, Protein engineering.

[21]  J Moult,et al.  Protein folding simulations with genetic algorithms and a detailed molecular description. , 1997, Journal of molecular biology.

[22]  J. Doye,et al.  Global Optimization by Basin-Hopping and the Lowest Energy Structures of Lennard-Jones Clusters Containing up to 110 Atoms , 1997, cond-mat/9803344.

[23]  Christoph Dellago,et al.  Efficient transition path sampling: Application to Lennard-Jones cluster rearrangements , 1998 .

[24]  Yehuda Zeiri,et al.  STRUCTURE AND DYNAMICS OF CL AND BR IONS AND ATOMS IN XE CLUSTERS , 1998 .

[25]  Wolfgang Quapp,et al.  A gradient-only algorithm for tracing a reaction path uphill to the saddle of a potential energy surface , 1996 .

[26]  Richard S. Judson,et al.  Analysis of the genetic algorithm method of molecular conformation determination , 1993, J. Comput. Chem..

[27]  K. Meiwes-Broer,et al.  Pure metal and metal-doped rare-gas clusters grown in a pulsed ARC cluster ion source , 1990 .

[28]  Bernd Hartke,et al.  Global geometry optimization of (Ar)n and B(Ar)n clusters using a modified genetic algorithm , 1996 .

[29]  J Moult,et al.  Genetic algorithms for protein structure prediction. , 1996, Current opinion in structural biology.

[30]  Poul Jørgensen,et al.  Geometrical derivatives of energy surfaces and molecular properties , 1986 .

[31]  Pinaki Chaudhury,et al.  A simulated annealing based technique for locating first-order saddle points on multidimensional surfaces and constructing reaction paths: several model studies , 1998 .

[32]  John Arthur Niesse,et al.  Global optimization of atomic and molecular clusters using the space‐fixed modified genetic algorithm method , 1997 .

[33]  P. Pulay,et al.  AB Initio Vibrational Force Fields , 1984 .

[34]  Yong L. Xiao,et al.  Genetic algorithm: a new approach to the prediction of the structure of molecular clusters , 1993 .

[35]  Zeiri Prediction of the lowest energy structure of clusters using a genetic algorithm. , 1995, Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics.

[36]  Jordi Mestres,et al.  Genetic algorithms: A robust scheme for geometry optimizations and global minimum structure problems , 1995, J. Comput. Chem..

[37]  K. Ho,et al.  Structural optimization of Lennard-Jones clusters by a genetic algorithm , 1996 .

[38]  M. Velegrakis,et al.  Structural transitions in metal ion-doped noble gas clusters: Experiments and molecular dynamics simulations , 1998 .

[39]  R Unger,et al.  Genetic algorithms for protein folding simulations. , 1992, Journal of molecular biology.

[40]  Wayne Pullan,et al.  Energy minimization of mixed argon–xenon microclusters using a genetic algorithm , 1997 .

[41]  P. Culot,et al.  A quasi-Newton algorithm for first-order saddle-point location , 1992 .

[42]  M. Velegrakis,et al.  Photofragmentation spectrum of the Sr+Ar complex , 1996 .

[43]  B. Hartke Global geometry optimization of clusters using genetic algorithms , 1993 .