Increasing the Time Step and Efficiency of Molecular Dynamics Simulations: Optimal Solutions for Equilibrium Simulations or Structure Refinement of Large Biomolecules

References

• Rahman , A. 1964 . "Correlations in the motion of atoms in liquid argon" . Phys. Rev. , 136A : 405
   Web of Science ®Google Scholar
• Allen , M.P. and Tildesley , DJ. 1987 . Computer Simulation of Liquids , Oxford : Clarendon Press .
   Google Scholar
• McCammon , J.A. , Gelin , B.R. and Karplus , M. 1977 . "Dynamics of folded proteins" . Nature , 267 : 585
   PubMed Web of Science ®Google Scholar
• van Gunsteren , W.F. and Beiendsen , H.J.C. 1990 . "Computer simulations of molecular dynamics: methodology, applications and perspectives in chemistry" . Angew. Chem., Int. Ed. Engl. , 29 : 992
   Web of Science ®Google Scholar
• Tieleman , O.P. , Marrink , S.J. and Berendsen , H.J.C. 1997 . "A computer perspective of membranes: Molecular dynamics studies of lipid bilayer systems" . Biochim. Biophys. Acta , 1331 : 235
   PubMed Web of Science ®Google Scholar
• van Gunsteren , W.F. , Kaptein , R. and Zuiderweg , E.R.P. "Use of molecular dynamics computer simulations when determining protein structure by 2D-NMR" . Proceedings NATO/CECAM Workshop on Nucleic Acid Conformation and Dynamics Orsay . pp. 79 – 97 . France : CECAM .
   Google Scholar
• Kaptein , R. , Zuiderweg , E.R.P. , Scheek , R.M. , Boelens , R. and van Gunsteren , W.F. 1985 . "A protein structure from nuclear magnetic resonance data, lac represser headpiece" . J. MoI. BioI. , 182 : 179
   PubMed Web of Science ®Google Scholar
• Brunger , A.T. and Nilges , M. 1993 . "Computational challenges for macromolecular structure determination by X-ray crystallography and solution NMR-spectroscopy" . Quart. Rev. Biophys. , 26 : 49
   PubMed Web of Science ®Google Scholar
• van Gunsteren , W.F. , Brunne , R.M. , Gros , P. , van Schaik , R.C. , Schiffer , C.A. and Torda , A.E. 1994 . "Accounting for molecular mobility in structure determination based on nuclear magnetic resonance spectroscopic and X-ray diffraction data" ” . In Methods in Enzymology: Nuclear Magnetic Resonance , Vol. 239 , 619 – 654 . New York : Academic Press .
   Google Scholar
• van Gunsteren , W.F. , Bonvin , A.M.J.J. , Daura , X. and Smith , L.J. 1999 . "Aspects of modeling biomolecular structure on the basis of spectroscopic or diffraction data" ” . In Structure Computation and Dynamics in Protein NMR, Biological Magnetic Resonance , Vol. 17 , 3 – 35 . New York : Plenum Press .
   Google Scholar
• Guntert , P. , Mumenthaler , C. and Wuthrich , K. 1997 . "Torsion angle dynamics for NMR structure calculation with the new program DYANA" . J. Mol. Biol. , 273 : 283
   PubMed Web of Science ®Google Scholar
• Stein , E.G. , Rice , L.M. and Brünger , A.T. 1997 . "Torsion-angle molecular dynamics as a new efficient tool for NMR structure calculation" . J. Magn. Res. , 124 : 154
   PubMed Web of Science ®Google Scholar
• Schuler , L.D. and van Gunsteren , W.F. 2000 . "On the choice of dihedral angle potential energy functions for n-alkanes" . Mol. Simulat. , 25 : 301
   Web of Science ®Google Scholar
• Rahman , A. and Stillinger , FH. 1971 . "Molecular dynamics study of liquid water" . J. Chem. Phys. , 55 : 3336
   Web of Science ®Google Scholar
• Berendsen , HJ.C. and van Gunsteren , W.F. 1984 . "Molecular dynamics simulations: techniques and approaches" ” . In Molecular Liquids-Dynamics and Interactions NATO ASI Series , Vol. C135 , 561 – 564 . Dordrecht : Reidel .
   Google Scholar
• van Gunsteren , W.F. , Boelens , R. , Kaptein , R. , Scheek , R.M. and Zuiderweg , E.R.P. 1985 . "An improved restrained molecular dynamics technique to obtain protein tertiary structure from nuclear magnetic resonance data" ” . In Molecular Dynamics and Protein Structure , 92 – 99 . Western Springs , , USA : Polycrystal Book Service . P.O. Box 27,, III . 60558,
   Google Scholar
• vanGunsteren , W.F. , Billeter , S.R. , Eising , A.A. , Hunenberger , PH. , Krüger , P. , Mark , A.E. , Scott , W.R.P. and Tironi , LG. 1996 . Biomolecular Simulation: The GROMOS96 Manual and User Guide , Zürich , , Switzerland : Vdf Hochschulverlag .
   Google Scholar
• van Gunsteren , WE and Karplus , M. 1982 . "Effect of constraints on the dynamics of macromolecules" . Macromolecules , 15 : 1528
   Web of Science ®Google Scholar
• Rice , L.M. and Brünger , A.T. 1994 . "Torsion angle dynamics: reduced variable conformational sampling enhances crystallographic structure refinement" . Proteins , 19 : 277
   PubMed Web of Science ®Google Scholar
• Levitt , M. , Hirshberg , M. , Sharon , R. , Laidig , K.E. and Daggett , V. 1997 . "Calibration and testing of a water model for simulation of the molecular dynamics of proteins and nucleic acids in solution" . J. Phys. Chem. B , 101 : 5051
   Web of Science ®Google Scholar
• Tuckerman , M. , Berne , B.J. and Martyna , G.J. 1992 . "Reversible multiple time scale molecular dynamics" . J. Chem. Phys. , 97 : 1990
   Web of Science ®Google Scholar
• Watanabe , M. and Karplus , M. 1993 . "Dynamics of molecules with internal degrees of freedom by multiple time-step methods" . J. Chem. Phys. , 99 : 8063
   Web of Science ®Google Scholar
• Izaguine , J.A. , Reich , S. and Skeel , R-D. 1999 . "Longer time steps for molecular dynamics" . J. Chem. Phys. , 110 : 9853
   Google Scholar
• Bennett , CH. 1975 . "Mass tensor molecular dynamics" . J. Comput. Phys. , 19 : 267
   Web of Science ®Google Scholar
• Ryckaert , J.-P. 1991 . Computer-Simulations in Material Science E205 of NATO ASI Series , Vol. E205 , 43 – 66 . Dordrecht : Kluwer Academic Publishers .
   Google Scholar
• Pomes , R. and McCammon , J.A. 1990 . "Mass and step length optimization for the calculation of equilibrium properties by molecular dynamics simulation" . Chem. Phys. Lett. , 166 : 425
   Web of Science ®Google Scholar
• Feenstra , K. , Hess , B. and Berendsen , H.J.C. 1999 . "Improving efficiency of large time-scale molecular dynamics simulations of hydrogen-rich systems" . J. Comput. Chem. , 20 : 786
   PubMed Web of Science ®Google Scholar
• Katz , H. , Walter , R. and Somorjay , R.L. 1979 . "Rotational dynamics of large molecules" . Comput. Chem. , 3 : 25
   Google Scholar
• Mazur , A.K. , Dorofeev , V.E. and Abagyan , R.A. 1991 . "Derivation and testing of explicit equations of motion for polymers described by internal coordinates" . J. Comput. Phys. , 92 : 261
   Web of Science ®Google Scholar
• Ryckaert , J.-R , Ciccotti , G. and Berendsen , H.J.C. 1977 . "Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes" . J. Comput. Phys. , 23 : 327
   Web of Science ®Google Scholar
• Ciccotti , G. , Ferrario , M. and Ryckaert , J.-P. 1982 . "Molecular dynamics of rigid systems in cartesian coordinates: a general formulation" . Mol. Phys. , 47 : 1253
   Web of Science ®Google Scholar
• Hess , B. , Bekker , H. , Berendsen , H.J.C. and Fraaije , J.G.E.M. 1997 . "LINCS: a linear constraint solver for molecular simulations" . J Comput. Chem. , 18 : 1463
   Web of Science ®Google Scholar
• Reich , S. 1995 . "Smoothed dynamics of highly oscillatory hamiltonian systems" . Physica D , 89 : 28
   Google Scholar
• van Gunsteren , W.F. , Huber , T. and Torda , A.E. "Biomolecular modelling: overview of types of methods to search and sample conformational space" . Conference Proceedings, American Institute of Physics, European Conference on Computational Chemistry . Vol. 330 , pp. 253 – 268 . E.C.C.C I .
   Google Scholar
• Frenkel , D. 1993 . Computer Simulation of Biomolecular Systems: Theoretical and Experimental Applications , Vol. 2 , 37 – 66 . Leiden , , The Netherlands : Escom .
   Google Scholar
• van Gunsteren , W.F. 1993 . "Molecular dynamics and stochastic dynamics simulation: a primer" ” . In Computer Simulation of Biomolecular systems, Theoretical and Experimental Applications , Vol. 2 , 3 – 36 . Leiden , , The Netherlands : Escom .
   Google Scholar
• Mazur , A.K. 1998 . "Hierarchy of motions in protein dynamics" . J. Phys. Chem. B , 102 : 473
   Web of Science ®Google Scholar
• van Gunsteren , W.F. 1991 . "Computer simulation of biomolecular systems: overview of time saving techniques" ” . In Advances in Biomolecular Simulations , Vol. 239 , 131 – 146 . American Institute of Physics .
   Google Scholar
• Scott , W.R.P. , Hunenberger , PH. , Tironi , I.G. , Mark , A.E. , Billeter , S.R. , Fennen , J. , Torda , A.E. , Huber , T. , Krüger , P. and van Gunsteren , W.F. 1999 . "The GROMOS biomolecular simulation program package" . J. Phys. Chem. A , 103 : 3596
   Web of Science ®Google Scholar
• Beutier , T.C. , Mark , A.E. , van Schaik , R.C. , Gerber , P.R. and van Gunsteren , W.F. 1994 . "Avoiding singularities and numerical instabilities in free energy calculations based on molecular simulations" . Chem. Phys. Letters , 222 : 529
   Web of Science ®Google Scholar
• Tironi , LG. , Sperb , R. , Smith , P.E. and van Gunsteren , W.F. 1995 . "A generalized reaction field method for molecular dynamics simulations" . J. Chem. Phys. , 102 : 5451
   Web of Science ®Google Scholar
• van Gunsteren , WE , Luque , F.J. , Timms , D. and Torda , A.E. 1994 . "Molecular mechanics in biology: from structure to function, taking account of solvation" . Ann. Rev. Biophys. Biomol. Struct. , 23 : 847
   PubMedGoogle Scholar
• Wittenburg , J. 1977 . Dynamics of Systems of Rigid Bodies , Stuttgart : Teubner .
   Google Scholar
• Bae , D.S. and Haug , E.J. 1987 . "A recursive formulation for constrained mechanical system dynamics: Part I. Open loop systems" . Mech. Struct. Mach. , 15 : 359
   Web of Science ®Google Scholar
• Bae , D.-S. and Haug , E.J. 1988 . "A recursive formulation for constrained mechanical system dynamics: Part II. Closed loop systems" . Mech. Struct. Mach. , 15 : 481
   Google Scholar
• Jain , A. , Vaidehi , N. and Rodriguez , G. 1993 . "A fast recursive algorithm for molecular dynamics simulation" . J. Comput. Phys. , 106 : 258
   Web of Science ®Google Scholar
• Turner , J.D. , Weiner , P.K. , Chun , H.M. , Lupi , V , Gallion , S. and Singh , U.C. 1993 . Computer Simulation of Biomolecular Systems: Theoretical and Experimental Applications , Vol. 2 , 535 – 555 . Leiden , , The Netherlands : Escom .
   Google Scholar
• Mathiowetz , A.M. , Jain , A. , Karasawa , N. and Goddard , W.A. III . 1994 . "Protein simulations using techniques suitable for very large systems: the cell multipole method for nonbonded interactions and the Newton-Euler inverse mass operator method for internal coordinate dynamics" . Proteins , 20 : 227
   PubMed Web of Science ®Google Scholar
• Goldstein , H. 1980 . Classical Mechanics, , 2nd ed. , Reading, MA , , USA : AddisonWesley .
   Google Scholar
• van Gunsteren , W.F. and Berendsen , H.J.C. 1977 . "Algorithms for macromolecular dynamics and constraint dynamics" . Mol. Phys. , 34 : 1311
   Web of Science ®Google Scholar
• Berendsen , H.J.C. and van Gunsteren , W.F. "Practical, algorithms for dynamic simulations" . Molecular-Dynamics Simulation of Statistical-Mechanical Systems Proceedings of the International School of Physics Enrico Fermi, Course 97 . pp. 43 – 65 . Amsterdam : North-Holland .
   Google Scholar
• Mazur , A.K. 1997 . "Common molecular dynamics algorithms revisited: Accuracy and optimal time steps of Störmerleapfrog integrators" . J. Comput. Phys. , 136 : 354
   Web of Science ®Google Scholar
• Hockney , R.W. and Eastwood , J.W. 1981 . Computer Simulation Using Particles , New York : McGraw-Hill .
   Google Scholar
• Verlet , L. 1967 . "Computer experiments on classical fluids. I thermodynamical properties of Lennard-Jones molecules" . Phys. Rev. , 159 : 98
   Web of Science ®Google Scholar
• van Gunsteren , W.F. 1980 . "Constrained dynamics of flexible molecules" . Mol. Phys. , 40 : 1015
   Web of Science ®Google Scholar
• Luty , B.A. , Davis , ME. , Tironi , I.G. and van Gunsteren , W.F. 1994 . "A comparison of particle-particle-particle-mesh and Ewald methods for calculating electrostatic interactions in periodic molecular systems" . Mol. Simulat. , 14 : 11
   Web of Science ®Google Scholar
• Berendsen , H.J.C. , Postrna , J.P.M. , van Gunsteren , W.F. , DiNola , A. and Haak , J.R. 1984 . "Molecular dynamics with coupling to an external bath" . J. Chem. Phys. , 81 : 3684
   Web of Science ®Google Scholar
• Bernstein , P.C. , Koetzle , T.F. , Williams , G.J.B. , Meyer , E.F. Jr , Brice , M.D. Jr , Rodgers , J.R. Jr , Kennard , O. Jr , Shimanouchi , T. Jr and Tasumi , M. Jr . 1977 . "The protein data bank: a computer-based archival file for macromolecular structures" . J. Mol. Biol. , 112 : 535
   PubMed Web of Science ®Google Scholar