References' Collection

Here a list of references you may want to citate

# Force Fields

## Compass

- Sun, H. Compass: An ab Initio Force Field Optimization for Condensed-Phase Applications- Overview with Details on Alkane and Benzene Compounds.
*J. Phys. Chem. B***1998**,*102*, 7338-77364

# MM/MD Methods

## Verlet Algorithm

- Verlet, L. Computer Experiments on Classical Fluids. I. Thermodynamic properties of Lennard-Jones Molecules.
*Phys. Rev***1967**,*159*, 98

# Software

## Gromacs

- Berendsen, et al. (1995)
*Comp. Phys. Comm.*91: 43-56. - Lindahl, et al. (2001)
*J. Mol. Model.*7: 306-317. - van der Spoel, et al. (2005)
*J. Comput. Chem.*26: 1701-1718. - Hess, et al. (2008)
*J. Chem. Theory Comput.*4: 435-447.

## TINKER

- P. Ren and J. W. Ponder,
*J. Phys. Chem. B*, 107, 5933-5947 (2003) - P. Ren and J. W. Ponder,
*J. Comput. Chem.*, 23, 1497-1506 (2002) - R. V. Pappu, R. K. Hart and J. W. Ponder,
*J. Phys. Chem. B*, 102, 9725-9742 (1998) - M. E. Hodsdon, J. W. Ponder and D. P. Cistola,
*J. Mol. Biol.*, 264, 585-602 (1996) - C. E. Kundrot, J. W. Ponder and F. M. Richards,
*J. Comput. Chem.*, 12, 402-409 (1991) - J. W. Ponder and F. M. Richards,
*J. Comput. Chem.*, 8, 1016-1024 (1987) - D. Beeman, "Some Multistep Methods for Use in Molecular Dynamics Calculations", Journal of Computational Physics, 20, 130-139 (1976)
- B. R. Brooks, "Algorithms for Molecular Dynamics at ConstantcTemperature and Pressure", DCRT Report, NIH, April 1988
- W. H. Press, S. A. Teukolsky, W. T. Vetterling and B. P. Flannery, Numerical Recipes (Fortran), 2nd Ed., Cambridge University Press, 1992, Section 3.6
- W. C. Still, A. Tempczyk, R. C. Hawley and T. Hendrickson, "A Semianalytical Treatment of Solvation for Molecular Mechanics and Dynamics", J. Amer. Chem. Soc., 112, 6127-6129 (1990) ("Onion" Method; see supplimentary material)
- D. Qiu, P. S. Shenkin, F. P. Hollinger and W. C. Still, "The GB/SA Continuum Model for Solvation. A Fast Analytical Method for the Calculation of Approximate Radii", J. Phys. Chem. A, 101, 3005-3014 (1997) (Analytical Still Method)
- G. D. Hawkins, C. J. Cramer and D. G. Truhlar, "Parametrized Models of Aqueous Free Energies of Solvation Based on Pairwise Descreening of Solute Atomic Charges from a Dielectric Medium", J. Phys. Chem., 100, 19824-19839 (1996) (HCT Method)
- A. Onufriev, D. Bashford and D. A. Case, "Exploring Protein Native States and Large-Scale Conformational Changes with a Modified Generalized Born Model", PROTEINS, 55, 383-394 (2004) (OBC Method)
- T. Grycuk, "Deficiency of the Coulomb-field Approximation in the Generalized Born Model: An Improved Formula for Born Radii Evaluation", J. Chem. Phys., 119, 4817-4826 (2003) (Grycuk Method)
- M. Schaefer, C. Bartels and M. Karplus, "Solution Conformations and Thermodynamics of Structured Peptides: Molecular Dynamics Simulation with an Implicit Solvation Model", J. Mol. Biol., 284, 835-848 (1998) (ACE Method)
- R. S. Martin, G. Peters and J. H. Wilkinson, Numerische Mathematik, 7, 362-383 (1965)
- M. L. Connolly, "Analytical Molecular Surface Calculation", Journal of Applied Crystallography, 16, 548-558 (1983)
- M. L. Connolly, "Computation of Molecular Volume", Journal of the American Chemical Society, 107, 1118-1124 (1985)
- G. Engeln-Mullges and F. Uhlig, Numerical Algorithms with Fortran, Springer Verlag, 1996, Section 10.1.2 [see routine "isplpe"]
- G. Engeln-Mullges and F. Uhlig, Numerical Algorithms with Fortran, Springer Verlag, 1996, Section 4.11.2
- W. H. Press, S. A. Teukolsky, W. T. Vetterling and B. P. Flannery, Numerical Recipes (Fortran), 2nd Ed., Cambridge University Press, 1992, Section 16.4
- U. Essmann, L. Perera, M. L Berkowitz, T. Darden, H. Lee and L. G. Pedersen, "A Smooth Particle Mesh Ewald Method", Journal of Chemical Physics, 103, 8577-8593 (1995)
- G. M. Crippen and T. F. Havel, "Distance Geometry and Molecular Conformation", Research Studies Press, Letchworth U.K., 1988, John Wiley and Sons, U.S. distributor
- T. F. Havel, "An Evaluation of Computational Strategies for Use in the Determination of Protein Structure from Distance Constraints obtained by Nuclear Magnetic Resonance", Progress in Biophysics and Molecular Biology, 56, 43-78 (1991)
- A. W. M. Dress and T. F. Havel, "Shortest-Path Problems and Molecular Conformation", Discrete Applied Mathematics, 19, 129-144 (1988)
- G. M. Crippen and T. F. Havel, "Distance Geometry and Molecular Conformation", Research Studies Press, Letchworth U.K., 1988, John Wiley and Sons, U.S. distributor, see section 6-2
- D. P. Bertsekas, "A Simple and Fast Label Correcting Algorithm for Shortest Paths", Networks, 23, 703-709 (1993)
- P. A. Steenbrink, "Optimization of Transport Networks", John Wiley and Sons, Bristol, 1974; see section 7.7
- R. Dionne, "Etude et Extension d'un Algorithme de Murchland", Infor, 16, 132-146 (1978)
- G. M. Crippen and T. F. Havel, "Stable Calculation of Coordinates from Distance Information", Acta Cryst., A34, 282-284 (1978)
- T. F. Havel, "An Evaluation of Computational Strategies for Use in the Determination of Protein Structure from Distance Constraints obtained by Nuclear Magnetic Resonance", Progress in Biophysics and Molecular Biology, 56, 43-78 (1991)
- C. M. Oshiro, J. Thomason and I. D. Kuntz, "Effects of Limited Input Distance Constraints Upon the Distance Geometry Algorithm", Biopolymers, 31, 1049-1064 (1991)
- A. E. Carlsson and S. Zapata, "The Functional Form of Angular Forces around Transition Metal Ions in Biomolecules", Biophysical Journal, 81, 1-10 (2001)
- J.-H. Lii and N. L. Allinger, "Directional Hydrogen Bonding in the MM3 Force Field. I", Journal of Physical Organic Chemistry, 7, 591-609 (1994)
- J.-H. Lii and N. L. Allinger, "Directional Hydrogen Bonding in the MM3 Force Field. II", Journal of Computational Chemistry, 19, 1001-1016 (1998)
- C. Sagui, L. G. Pedersen and T. A. Darden, "Towards an Accurate Representation of Electrostatics in Classical Force Fields: Efficient Implementation of Multipolar Interactions in Biomolecular Simulations", Journal of Chemical Physics, 120, 73-87 (2004)
- W. Smith, "Point Multipoles in the Ewald Summation (Revisited)", CCP5 Newsletter, 46, 18-30, 1998 (see http://www.ccp5.org/)
- W. J. Cody, "Rational Chebyshev Approximations for the Error Function", Mathematics of Computation, 631-638, 1969
- Y. Kong and J. W. Ponder, "Reaction Field Methods for Off-Center Multipoles", Journal of Chemical Physics, 107, 481-492 (1997)
- J. Ma and J. E. Straub, "Simulated Annealing using the Classical Density Distribution", Journal of Chemical Physics, 101, 533-541 (1994)
- Herbert Goldstein, "Classical Mechanics, 2nd Edition", Addison-Wesley, Reading, MA, 1980; see the Euler angle xyz convention in Appendix B
- K. L. Majumder and G. P. Bhattacharjee, "Inverse of the Incomplete Beta Function Ratio", Applied Statistics, 22, 411-414 (1973)
- L. Wesson and D. Eisenberg, "Atomic Solvation Parameters Applied to Molecular Dynamics of Proteins in Solution", Protein Science, 1, 227-235 (1992) (Eisenberg-McLachlan ASP)
- T. Ooi, M. Oobatake, G. Nemethy and H. A. Scheraga, "Accessible Surface Areas as a Measure of the Thermodynamic Parameters of Hydration of Peptides", PNAS, 84, 3086-3090 (1987) (SASA)
- M. Schaefer, C. Bartels, F. Leclerc and M. Karplus, "Effective Atom Volumes for Implicit Solvent Models: Comparison between Voronoi Volumes and Minimum Fluctuations Volumes", Journal of Computational Chemistry, 22, 1857-1879 (2001) (ACE)
- J. Nocedal, "Updating Quasi-Newton Matrices with Limited Storage", Mathematics of Computation, 35, 773-782 (1980)
- D. C. Lui and J. Nocedal, "On the Limited Memory BFGS Method for Large Scale Optimization", Mathematical Programming, 45, 503-528 (1989)
- J. Nocedal and S. J. Wright, "Numerical Optimization", Springer-Verlag New York, 1999, Section 9.1
- F. Sullivan, R. D. Mountain and J. O'Connell, "Molecular Dynamics on Vector Computers", Journal of Computational Physics, 61, 138-153 (1985)
- P. W. Atkins, "Physical Chemistry, 4th Edition", W. H. Freeman, New York, 1990; see section 24.2 for general discussion.
- Z. Li and H. A. Scheraga, "Monte Carlo-Minimization Approach to the Multiple-Minima Problem in Protein Folding", Proc. Natl. Acad. Sci. USA, 84, 6611-6615 (1987)
- R. Lavery, K. Zakrzewska, "Base and Base Pair Morphologies, Helical Parameters, and Definitions" in "Oxford Handbook of Nucleic Acid Structure", S. Neidel, Editor, Oxford University Press, 1999, pages 40-42
- W. Saenger, "Principles of Nucleic Acid Structure", Springer-Verlag, 1984, page 52
- W. C. Davidon, "Optimally Conditioned Optimization Algorithms Without Line Searches", Mathematical Programming, 9, 1-30 (1975)
- D. F. Shanno and K-H. Phua, "Matrix Conditioning and Nonlinear Optimization", Mathematical Programming, 14, 149-16 (1977)
- D. F. Shanno and K-H. Phua, "Numerical Comparison of Several Variable-Metric Algorithms", Journal of Optimization Theory and Applications, 25, 507-518 (1978)
- Herbert Goldstein, "Classical Mechanics, 2nd Edition", Addison-Wesley, Reading, MA, 1980; see the Euler angle xyz convention in Appendix B
- D. B. Cook, "Structures and Approximations for Electrons in Molecules", Ellis Horwood Limited, Sussex, England, 1978, adapted from the code in Chapter 7
- R. Czerminski and R. Elber, "Reaction Path Study of Conformational Transitions in Flexible Systems: Applications to Peptides", Journal of Chemical Physics, 92, 5580-5601 (1990)
- H. J. C. Berendsen, J. P. M. Postma, W. F. van Gunsteren, A. DiNola and J. R. Hauk, "Molecular Dynamics with Coupling to an External Bath", Journal of Chemical Physics, 81, 3684-3690 (1984)
- S. E. Feller, Y. Zhang, R. W. Pastor, B. R. Brooks, "Constant Pressure Molecular Dynamics Simulation: The Langevin Piston Method", Journal of Chemical Physics, 103, 4613-4621 (1995)
- D. Frenkel and B. Smit, "Understanding Molecular Simulation, 2nd Edition", Academic Press, San Diego, CA, 2002; Section 5.4 original version written by Alan Grossfield, January 2004;
- J. Kostrowicki and H. A. Scheraga, "Application of the Diffusion Equation Method for Global Optimization to Oligopeptides", Journal of Physical Chemistry, 96, 7442-7449 (1992)
- S. Nakamura, H. Hirose, M. Ikeguchi and J. Doi, "Conformational Energy Minimization Using a Two-Stage Method", Journal of Physical Chemistry, 99, 8374-8378 (1995)
- S. K. Kearsley, "On the Orthogonal Transformation Used for Structural Comparisons", Acta Crystallographica Section A, 45, 208-210 (1989)
- P. L'Ecuyer, Communications of the ACM, 31, 742-774 (1988)
- W. H. Press, S. A. Teukolsky, W. T. Vetterling and B. P. Flannery, Numerical Recipes (Fortran), 2nd Ed., Cambridge University Press, 1992, Section 7.1
- G. Marsaglia, Ann. Math. Stat., 43, 645 (1972) R. C. Rapaport, The Art of Molecular Dynamics Simulation, 2nd Edition, Cambridge University Press, 2004, Section 18.4
- E. B. Saff and A. B. J. Kuijlaars, "Distributing Many Points on a Sphere", The Mathematical Intelligencer, 19, 5-11 (1997)
- H. C. Andersen, "RATTLE: A Velocity Version of the SHAKE Algorithm for Molecular Dynamics Calculations", Journal of Computational Physics, 52, 24-34 (1983)
- W. Smith, "Hail Euler and Farewell: Rotational Motion in the Laboratory Frame", CCP5 Newsletter, February 2005
- M. P. Allen, "Brownian Dynamics Simulation of a Chemical Reaction in Solution", Molecular Physics, 40, 1073-1087 (1980)
- F. Guarnieri and W. C. Still, "A Rapidly Convergent Simulation Method: Mixed Monte Carlo/Stochastic Dynamics", Journal of Computational Chemistry, 15, 1302-1310 (1994)
- S. Yun-Yi, W. Lu and W. F. van Gunsteren, "On the Approximation of Solvent Effects on the Conformation and Dynamics of Cyclosporin A by Stochastic Dynamics Simulation Techniques", Molecular Simulation, 1, 369-383 (1988)
- A. O. Griewank, "Generalized Descent for Global Optimization", Journal of Optimization Theory and Applications, 34, 11-39 (1981)
- R. A. R. Butler and E. E. Slaminka, "An Evaluation of the Sniffer Global Optimization Algorithm Using Standard Test Functions", Journal of Computational Physics, 99, 28-32 (1992)
- J. W. Rogers, Jr. and R. A. Donnelly, "Potential Transformation Methods for Large-Scale Global Optimization", SIAM Journal of Optimization, 5, 871-891 (1995)
- T. J. Richmond, "Solvent Accessible Surface Area and Excluded Volume in Proteins", Journal of Molecular Biology, 178, 63-89 (1984)
- L. Wesson and D. Eisenberg, "Atomic Solvation Parameters Applied to Molecular Dynamics of Proteins in Solution", Protein Science, 1, 227-235 (1992)
- D. Frenkel and B. Smit, "Understanding Molecular Simulation, 2nd Edition", Academic Press, San Diego, CA, 2002; see Appendix E.2 for implementation details
- G. J. Martyna, M. E. Tuckerman, D. J. Tobias and M. L. Klein, "Explicit Reversible Integrators for Extended Systems Dynamics", Molecular Physics, 87, 1117-1157 (1996)
- H. J. C. Berendsen, J. P. M. Postma, W. F. van Gunsteren, A. DiNola and J. R. Hauk, "Molecular Dynamics with Coupling to an External Bath", Journal of Chemical Physics, 81, 3684-3690 (1984)
- G. Bussi and M. Parrinello, "Stochastic Thermostats: Comparison of Local and Global Schemes", Computer Physics Communications, 179, 26-29 (2008)
- H. C. Andersen, "Molecular Dynamics Simulations at Constant Pressure and/or Temperature", Journal of Chemical Physics, 72, 2384-2393 (1980)
- J. W. Ponder and F. M Richards, "An Efficient Newton-like Method for Molecular Mechanics Energy Minimization of Large Molecules", Journal of Computational Chemistry, 8, 1016-1024 (1987)
- R. S. Dembo and T. Steihaug, "Truncated-Newton Algorithms for Large-Scale Unconstrained Optimization", Mathematical Programming, 26, 190-212 (1983)
- P. L. Popelier and A. J. Stone, "Formulae for the First and Second Derivatives of Aniostropic Potentials with Respect to Geometrical Parameters", Molecular Physics, 82, 411-425 (1994)
- C. Murray, S. C. Racine and E. R. Davidson, "Improved Algorithms for the Lowest Few Eigenvalues and Associated Eigenvectors of Large Matrices", Journal of Computational Physics, 103, 382-389 (1992)
- A. L. Kaledin, "Gradient-Based Direct Normal-Mode Analysis", Journal of Chemical Physics, 122, 184106 (2005)
- A. L. Kaledin, M. Kaledin and J. M. Bowman, "All-Atom Calculation of the Normal Modes of Bacteriorhodopsin Using a Sliding Block Iterative Diagonalization Method", Journal of Chemical Theory and Computation, 2, 166-174 (2006)
- M. Levitt, C. Sander and P. S. Stern, "Protein Normal-mode Dynamics: Trypsin Inhibitor, Crambin, Ribonuclease and Lysozyme", Journal of Molecular Biology, 181, 423-447 (1985)
- C. E. Kundrot, J. W. Ponder and F. M. Richards, "Algorithms for Calculating Excluded Volume and Its Derivatives as a Function of Molecular Conformation and Their Use in Energy Minimization", Journal of Computational Chemistry, 12, 402-409 (1991)

Suggested reading from the TINKER developed are here