References ========== This section contains a list of the references to general theory, algorithms and implementation details which have been of use during the development of the Tinker package. Methods described in some of the references have been implemented in detail within the Tinker source code. Other references contain useful background information although the algorithms themselves are now obsolete. Still other papers contain ideas or extensions planned for future inclusion in Tinker. References for specific force field parameter sets are provided in an earlier section of this User's Guide. This list is heavily skewed toward biomolecules in general and proteins in particular. This bias reflects our group's major interests; however an attempt has been made to include methods which should be generally applicable. Molecular Mechanics & Dynamics Software Packages ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Tinker Software Tools --------------------- **Tinker** Tinker 8: Software Tools for Molecular Design, J. A. Rackers, Z. Wang, C. Lu, M. L. Laury, L. Lagardere, M. J. Schnieders, J.-P. Piquemal, P. Ren and J. W. Ponder, J. Chem. Theory Comput., 14, 5273-5289 (2018) **Tinker-HP** Tinker-HP: A Massively Parallel Molecular Dynamics Package for Multiscale Simulations of Large Complex Systems with Advanced Point Dipole Polarizable Force Fields, L. Lagardere, L.-H. Jolly, F. Lipparini, F. Aviat, B. Stamm, Z. F. Jing, M. Harger, H. Torabifard, G. A. Cisneros, M. J. Schnieders, N. Gresh, Y. Maday, P. Y. Ren, J. W. Ponder and J.-P. Piquemal, Chem. Sci., 9, 956-972 (2018) **Tinker-OpenMM** Tinker-OpenMM: Absolute and Relative Alchemical Free Energies Using AMOEBA on GPUs, M. Harger, D. Li, Z. Wang, K. Dalby, L. Lagardere, J.-P. Piquemal, J. Ponder and P. Ren, J. Comput. Chem., 38, 2047-2055 (2017) Alternative Molecular Modeling Software --------------------------------------- .. code-block:: text AMBER Peter Kollman, University of California, San Francisco AMMP Robert Harrison, Georgia State University, Atlanta ARGOS J. Andrew McCammon, University of California, San Diego BOSS William Jorgensen, Yale University BRUGEL Shoshona Wodak, Free University of Brussels CFF Shneior Lifson, Weizmann Institute CHARMM Martin Karplus, Harvard University DELPHI Bastian van de Graaf, Delft University of Technology DISCOVER Molecular Simulations Inc., San Diego DL_POLY Ilian Todorov & W. Smith, STFC Daresbury Laboratory ECEPP Harold Scheraga, Cornell University ENCAD Michael Levitt, Stanford University FANTOM Werner Braun, University of Texas, Galveston FEDER/2 Nobuhiro Go, Kyoto University GROMACS Erik Lindahl, Stockholm University GROMOS Wilfred van Gunsteren, BIOMOS and ETH, Zurich IMPACT Ronald Levy, Temple University, Philadelphia MACROMODEL Schodinger, Inc., New York MM2/MM3/MM4 N. Lou Allinger, University of Georgia MMC Cliff Dykstra, Indiana Univ.-Purdue Univ. at Indianapolis MMFF Thomas Halgren, Merck Research Laboratories, Rahway, NJ MMTK Konrad Hinsen, Inst. of Structural Biology, Grenoble MOIL Ron Elber, Cornell University MOLARIS Arieh Warshel, University of Southern California MOLDY Keith Refson, Oxford University MOSCITO Dietmar Paschek & Alfons Geiger, Universitat Dortmund NAMD Klaus Schulten, University of Illinois, Urbana OOMPAA J. Andrew McCammon, University of California, San Diego OPENMM Peter Eastman & Vijay Pande, Stanford University ORAL Karel Zimmerman, INRA, Jouy-en-Josas, France ORIENT Anthony Stone, Cambridge University PCMODEL Kevin Gilbert, Serena Software, Bloomington, Indiana PEFF Jan Dillen, University of Pretoria, South Africa PHENIX Paul Adams, Lawrence Berkeley Laboratory Q Johan Aqvist, Uppsala University SIBFA Nohad Gresh, INSERM, CNRS, Paris SIGMA Jan Hermans, University of North Carolina SPASIBA Gerard Vergoten, Universite de Lille SPASMS David Spellmeyer and the Kollman Group, UCSF UTAH5 Cornelis Altona, Leiden University, Netherlands XPLOR/CNS Axel Brunger, Stanford University YAMMP Stephen Harvey, University of Alabama, Birmingham YASP Florian Mueller-Plathe, TU Darmstadt YETI Angelo Vedani, Biografik-Labor 3R, Basel **AMBER** An Overview of the Amber Biomolecular Simulation Package, R. Salomon-Ferrer, D. A. Case, R. C. Walker, WIREs Comput. Mol. Sci. 3, 198-210 (2013) The Amber Biomolecular Simulation Programs. D. A. Case, T. E. Cheatham, III, T. Darden, H. Gohlke, R. Luo, K. M. Merz, Jr., A. Onufriev, C. Simmerling, B. Wang and R. Woods. J. Comput. Chem., 26, 1668-1688 (2005) AMBER, a Package of Computer Programs for Applying Molecular Mechanics, Normal Mode Analysis, Molecular Dynamics and Free Energy Calculations to Simulate the Structural and Energetic Properties of Molecules, D. A Pearlman, D. A. Case, J. W. Caldwell, W. S. Ross, T. E. Cheatham III, S. DeBolt, D. Ferguson, G. Seibel and P. Kollman, Comp. Phys. Commun., 91, 1-41 (1995) **AMMP** Stiffness and Energy Conservation in Molecular Dynamics: An Improved Integrator, R. W. Harrison, J. Comput. Chem., 14, 1112-1122 (1993) **ARGOS** ARGOS, a Vectorized General Molecular Dynamics Program, T. P. Straatsma and J. A. McCammon, J. Comput. Chem., 11, 943-951 (1990) **BOSS** Molecular Modeling of Organic and Biomolecular Systems Using BOSS and MCPRO, W. L. Jorgensen and J. Tirado-Rives, J. Comput. Chem., 26, 1689-1700 (2005) **BRUGEL** Interactive Computer Animation of Macromolecules, P. Delhaise, M. Bardiaux and S. Wodak, J. Mol. Graphics, 2, 103-106 (1984) **CHARMM** CHARMM: The Biomolecular Simulation Program, B. R. Brooks, C. L. Brooks III, A. D. Mackerell, L. Nilsson, R. J. Petrella, B. Roux, Y. Won, G. Archontis, C. Bartels, S. Boresch A. Caflisch, L. Caves, Q. Cui, A. R. Dinner, M. Feig, S. Fischer, J. Gao, M. Hodoscek, W. Im, K. Kuczera, T. Lazaridis, J. Ma, V. Ovchinnikov, E. Paci, R. W. Pastor, C. B. Post, J. Z. Pu, M. Schaefer, B. Tidor, R. M. Venable, H. L. Woodcock, X. Wu, W. Yang, D. M. York, and M. Karplus, J. Comput. Chem., 30, 1545-1615 (2009) CHARMM: The Energy Function and Its Parameterization with an Overview of the Program, A. D. MacKerell, Jr., B. Brooks, C. L. Brooks, III, L. Nilsson, B. Roux, Y. Won, and M. Karplus, in The Encyclopedia of Computational Chemistry, Vol. 1, pg. 271-277, John Wiley & Sons, Chichester, 1998 CHARMM: A Program for Macromolecular Energy, Minimization, and Dynamics Calculations, B. R. Brooks, R. E. Bruccoleri, B. D. Olafson, D. J. States, S. Swaminathan and M. Karplus, J. Comput. Chem., 4, 187-217 (1983) **DELPHI** Delft Molecular Mechanics: A New Approach to Hydrocarbon Force Fields. Inclusion of a Geometry-Dependent Charge Calculation, A. C. T. van Duin, J. M. A. Baas and B. van de Graaf, J. Chem. Soc. Faraday Trans., 90, 2881-2895 (1994) **DL_POLY** DL_POLY_3: New Dimensions in Molecular Simulations via Massive Parallelism, I. T. Todorov, W. Smith, K. Trachenko and M. T. Dove, J. Mater. Chem., 16, 1911-1918 (2006) **ENCAD** Potential Energy Function and Parameters for Simulations for the Molecular Dynamics of Proteins and Nucleic Acids in Solution, M. Levitt, M. Hirshberg, R. Sharon and V. Daggett, Comp. Phys. Commun., 91, 215-231 (1995) **FANTOM** The Program FANTOM for Energy Refinement of Polypeptides and Proteins Using a Newton-Raphson Minimizer in Torsion Angle Space, T. Schaumann, W. Braun and K. Wurtrich, Biopolymers, 29, 679-694 (1990) **FEDER/2** FEDER/2: Program for Static and Dynamic Conformational Energy Analysis of Macro-molecules in Dihedral Angle Space, H. Wako, S. Endo, K. Nagayama and N. Go, Comp. Phys. Commun., 91, 233-251 (1995) **GROMACS** GROMACS: High Performance Molecular Simulations Through Multi-Level Parallelism from Laptops to Supercomputers, M. J. Abraham, T. Murtola, R. Schultz, S. Pall, J. C. Smith, B. Hess and E. Lindahl, SoftwareX, 1-2, 19-25 (2015) GROMACS 4.5: A High-Throughput and Highly Parallel Open Source Molecular Simulation Toolkit, S. Pronk, S. Pall, R. Schulz, P. Larsson, P. Bjelkmar, R. Apostolov, M. R. Shirts, J. C. Smith, P. M. Kasson, D. van der Spoel, B. Hess and E. Lindahl, Bioinformatics, 29, 845-854 (2013) GROMACS 3.0: A Package for Molecular Simulation and Trajectory Analysis, E. Lindahl, B. Hess and D. van der Spoel, J. Mol. Model., 7, 306-317 (2001) **GROMOS** The GROMOS Biomolecular Simulation Program Package, W. R. P. Scott, P. H. Hunenberger , I. G. Tironi, A. E. Mark, S. R. Billeter, J. Fennen, A. E. Torda, T. Huber, P. Kruger, W. F. van Gunsteren, J. Phys. Chem. A, 103, 3596-3607 (1999) **IMPACT** Integrated Modeling Program, Applide Chemical Theory (IMPACT), J. L. Banks, H. S. Beard, Y. Cao, A. E. Cho, W. Damm, R. Farid, A. K. Felts, T. A. Halgren, D. T. Mainz, J. R. Maple, R. Murphy, D. M. Philipp, M. P. Repasky, L. Y. Zhang, B. J. Berne, R. A. Friesner, E. Gallicchio and R. M. Levy, J. Comput. Chem., 26, 1752-1780 (2005) **MACROMODEL** MacroModel: An Integrated Software System for Modeling Organic and Bioorganic Molecules Using Molecular Mechanics, F. Mahamadi, N. G. J. Richards, W. C. Guida, R. Liskamp, M. Lipton, C. Caufield, G. Chang, T. Hendrickson and W. C. Still, J. Comput. Chem., 11, 440-467 (1990) **MM2** Conformational Analysis. 130. MM2. A Hydrocarbon Force Field Utilizing V1 and V2 Torsional Terms, N. L. Allinger, J. Am. Chem. Soc., 99, 8127-8134 (1977) **MM3** Molecular Mechanics. The MM3 Force Field for Hydrocarbons, N. L. Allinger, Y. H. Yuh and J.-H. Lii, J. Am. Chem. Soc., 111, 8551-8566 (1989) **MM4** An Improved Force Field (MM4) for Saturated Hydrocarbons, N. L. Allinger, K. Chen and J.-H. Lii, J. Comput. Chem., 17, 642-668 (1996) **MMC** Molecular Mechanics for Weakly Interacting Assemblies of Rare Gas Atoms and Small Molecules, C. E. Dykstra, J. Am. Chem. Soc., 111, 6168-6174 (1989) **MMFF** Merck Molecular Force Field. I. Basis, Form, Scope, Parameterization, and Performance of MMFF94, T. A. Halgren, J. Comput. Chem., 17, 490-516 (1996) **MOIL** MOIL: A Program for Simulations of Macromolecules, R. Elber, A. Roitberg, C. Simmerling, R. Goldstein, H. Li, G. Verkhiver, C. Keasar, J. Zhang and A. Ulitsky, Comp. Phys. Commun., 91, 159-189 (1995) **MOSCITO** Information available at the site http://139.30.122.11/MOSCITO/ **NAMD** Scalable Molecular Dynamics with NAMD, J. C. Phillips, R. Braun, W. Wang, J. Gumbart, E. Tajkhorshid, E. Villa, C. Chipot, R. D. Skeel, L. Kale and K. Schulten, J. Comput. Chem., 26, 1781-1802 (2005) **OOMPAA** OOMPAA: Object-oriented Model for Probing Assemblages of Atoms, G. A. Huber and J. A. McCammon, J. Comput. Phys., 151, 264-282 (1999) **ORAL** ORAL: All Purpose Molecular Mechanics Simulator and Energy Minimizer, K. Zimmermann, J. Comput. Chem., 12, 310-319 (1991) **ORIENT** Orient: A Program for Studying Interactions Between Molecules, Version 5.0, A. J. Stone, A. Dullweber, O. Engkvist, E. Fraschini, M. P. Hodges, A. W. Meredith, D. R. Nutt, P. L. A. Popelier and D. J. Wales, University of Cambridge, 2018 Information available at the site http://www-stone.ch.cam.ac.uk/programs.html#Orient/ **PCMODEL** PCMODEL V9.0: Molecular Modeling Software, User's Manual, Serena Software, Bloomington, IN, 2004 **PEFF** PEFF: A Program for the Development of Empirical Force Fields, J. L. M. Dillen, J. Comput. Chem., 13, 257-267 (1992) **PHENIX** Macromolecular Structure Determination Using X-rays, Neutrons and Electrons: Recent Developments in Phenix, D. Liebschner, P. V. Afonine, M. L. Baker, G. Bunkóczi, V. B. Chen, T. I. Croll, B. Hintze, L.-W. Hung, S. Jain, A. J. McCoy, N. W. Moriarty, R. D. Oeffner, B. K. Poon, M. G. Prisant, R. J. Read, J. S. Richardson, D. C. Richardson, M. D. Sammito, O. V. Sobolev, D. H. Stockwell, T. C. Terwilliger, A. G. Urzhumtsev, L. L. Videau, C. J. Williams and P. D. 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