# References

- [Bondi1964]
  A. Bondi
  van der Waals Volumes and Radii
  J. Phys. Chem. 68, 441-451 (1964)
- [DPMTA]
  William T. Rankin
  DPMTA - A Distributed Implementation of the Parallel Multipole Tree Algorithm - Version 3.0
  http://www.ee.duke.edu/Research/SciComp/Docs/Dpmta/users_guide/dpmta.html
- [Eisenhaber1993]
  F. Eisenhaber, P. Argos
  Improved Strategy in Analytic Surface Calculation for Molecular Systems: Handling of Singularities and Computational Efficiency
  J. Comp. Chem. 14(11), 1272-1280 (1993)
- [Eisenhaber1995]
  F. Eisenhaber, P. Lijnzaad, P. Argos, M. Scharf
  The Double Cubic Lattice Method: Efficient Approaches to Numerical Integration of Surface Area and Volume and to Dot Surface Contouring of Molecular Assemblies
  J. Comp. Chem. 16(3), 273-284 (1995)
- [Hinsen1995]
  Konrad Hinsen, Gerald R. Kneller
  Influence of constraints on the dynamics of polypeptide chains
  Phys. Rev. E 52, 6868 (1995)
- [Hinsen1997]
  Konrad Hinsen, Benoit Roux
  An accurate potential for simulating proton transfer in acetylacetone
  J. Comp. Chem. 18, 368 (1997)
- [Hinsen1998]
  Konrad Hinsen
  Analysis of domain motions by approximate normal mode calculations
  Proteins 33(3), 417-429 (1998)
- [Hinsen1999]
  Konrad Hinsen, Aline Thomas, Martin J. Field
  Analysis of domain motions in large proteins
  Proteins 34(3), 369-382 (1999)
- [Hinsen1999a]
  Konrad Hinsen, Gerald R. Kneller
  Projection methods for the analysis of complex motions in macromolecules
  Molecular Simulations 23(3), 203-241 (1999)
- [Hinsen1999b]
  Konrad Hinsen, Gerald R. Kneller
  A simplified force field for describing vibrational protein dynamics over the whole frequency range
  J. Chem. Phys. 111(24), 10766-10769 (1999)
- [Hinsen2000]
  Konrad Hinsen, Andrei J. Petrescu, Serge Dellerue, Marie-Claire Bellissent-Funel, Gerald R. Kneller
  Harmonicity in slow protein dynamics
  submitted
- [Kneller1990]
  Gerald R. Kneller
  Superposition of molecular structures using quaternions
  Mol. Sim. 7, 113-119 (1990)
- [Kneller1996]
  Gerald R. Kneller, Thomas Mülders
  Nosé-Andersen dynamics of partially rigid molecules: Coupling of all degrees of freedom to heat and pressure baths
  Phys. Rev. E 54, 6825-6837 (1996)
- [Swope1982]
  W.C. Swope, H.C. Andersen, P.H. Berens, K.R. Wilson
  A computer simulation method for the calculation of equilibrium constants for the formation of physical clusters of molecules: application to small water clusters
  J. Chem. Phys. 76, 637--649 (1982)
- [vanGunsteren1982]
  Wilfred F. van Gunsteren, Martin Karplus
  Effect of Constraints on the Dynamics of Macromolecules
  Macromolecules 15, 1528-1544 (1982)
- [Viduna2000]
  David Viduna, Konrad Hinsen, Gerald R. Kneller
  The influence of molecular flexibility on DNA radiosensitivity: A simulation study
  Phys. Rev. E, in print
- [Wolf1999]
  D. Wolf, P. Keblinski, S.R. Philpot, J. Eggebrecht
  Exact method for the simulation of Coulombic systems by spherically truncated, pairwise r-1 summation
  J. Chem. Phys. 110(17), 8254-8282 (1999)