

The principle sources of documentation for the module library may be found in:
- The paper M. J. Field, M. Albe, C. Bret, F. Proust-De Martin and A. Thomas, The DYNAMO
Library for Molecular Simulations using Hybrid Quantum Mechanical and Molecular Mechanical Potentials, Journal of Computational
Chemistry, 21, 1088-1100, 2000. This paper describes the semi-empirical QM and hybrid potential capabilities of the
program.
Examples of studies performed wholly or partially with the DYNAMO library include:
- A. Thomas, D. Jourand, C. Bret, P. Amara and M. J. Field, Is There a Covalent Intermediate
in the Viral Neuraminidase Reaction? A Hybrid-Potential Free-Energy Study, J. Amer. Chem. Soc., 121, 1999,
9693-9702.
- C. Bret, M. J. Field and L. Hemmingsen. A Chemical Potential Equalization Model for Treating Polarization in
Molecular Mechanical Force Fields, Mol. Phys., 98, 2000, 751-763.
- F. Proust-De Martin, R. Dumas and M. J. Field. A Hybrid-Potential Free-Energy Study of the Isomerization
Step of the Acetohydroxy Acid Isomeroreductase Reaction. J. Amer. Chem. Soc., 122, 2000, 7688-7697.
- S. Martí, J. Andrés, V. Moliner, E. Silla, I. Tuñón, J. Bertrán and M. J.
Field. Insights into Enzyme Catalysis: The Chorismate Mutase Case. J. Amer. Chem. Soc., 123, 2001, 1709-1712.
- E. Pellegrini and M. J. Field. A Generalized Born Solvation Model for Macromolecular Hybrid-Potential
Calculations. J. Phys. Chem. A, 106, 2002, 1316-1326.
- A. Thomas and M. J. Field. Reaction Mechanism of the HGXPRTase from Plasmodium falciparum: A Hybrid
Potential Quantum Mechanical/Molecular Mechanical Study. J. Amer. Chem. Soc., 124, 2002, 12432-12438.
- P. Amara and M. J. Field. Evaluation of an Ab Initio QM/MM Hybrid-Potential Link-Atom Method.
Theor. Chem. Accts., 109, 2003, 43-52.
- T. Wymore, D. W. Deerfield II, M. J. Field, J. Hempel and H. B. Nicholas, Jr. Initial Catalytic Events in
Class 3 Aldehyde Dehydrogenase: MM and QM/MM Simulations. Chemico-Biological Interactions 143/144, 2003, 75-84.
- M. Oliva, O. Dideberg and M. J. Field. Understanding the Molecular Mechanims of Active-Site Serine
Penicillin-Recognizing Proteins: A Molecular Dynamics Simulations Study. Proteins: Structure, Function and Genetics, 58, 88-100,
2003.
There are a number of discrepancies between the version of the DYNAMO library described in the book and the
current version. The changes are largely cosmetic as the functionality and the way of performing the calculations remain
much the same. The principle differences are:
There are also a number of new features, apart from those related to the QM parts of the program, that have been
added since the book was written. These include:
- The subroutine Atoms_Fix in the module Atoms module can be used to fix the positions of atoms so that they do not move during
a geometry optimization or a molecular dynamics calculation.
- The module Atom_Manipulation has procedures for the identification and
selection of atoms.
- The module Build_Coordinates can estimate the positions of undefined
hydrogens.
- The module Dynamics_Langevin_Verlet performs Langevin molecular
dynamics algorithms.
- The module Dynamics_Leapfrog_Verlet does molecular dynamics
simulations using a leap-frog algorithm.
- The module XYZ_IO has procedures that read and write coordinate files in XYZ
format.