Acknowledgments¶
The Tinker package has developed over a period of many years, very slowly during the late-1980s, and more rapidly since the mid-1990s in Jay Ponder’s research group at the Washington University School of Medicine in Saint Louis. Many people have played significant roles in the development of the package into its current form. The major contributors are listed below:
Stew Rubenstein
coordinate interconversions; original optimization methods and torsional angle manipulation
Craig Kundrot
molecular surface area & volume and their derivatives
Shawn Huston
original Amber/OPLS implementation; free energy calculations; time correlation functions
Mike Dudek
initial multipole models for peptides and proteins
Yong “Mike” Kong
multipole electrostatics; dipole polarization; reaction field treatment; Tinker water model
Reece Hart
potential smoothing methodology; Scheraga’s DEM, Straub’s GDA and extensions
Mike Hodsdon
extension of the Tinker distance geometry program and its application to NMR NOE structure determination
Rohit Pappu
potential smoothing methodology and PSS algorithms; rigid body optimization; GB/SA solvation derivatives
Wijnand Mooij
MM3 directional hydrogen bonding term; crystal lattice minimization code
Gerald Loeffler
stochastic/Langevin dynamics implementation
Marina Vorobieva & Nina Sokolova
nucleic acid building module and parameter translation
Peter Bagossi
AMOEBA force field parameters for alkanes and diatomics
Pengyu Ren
Ewald summation for polarizable atomic multipoles; AMOEBA force field for water, organics and peptides
Anders Carlsson
original ligand field potential energy term for transition metals
Andrey Kutepov
integrator for rigid-body dynamics trajectories
Tom Darden
Particle Mesh Ewald (PME) code, and development of PME for the AMOEBA force field
Alan Grossfield
Monte Carlo minimization; tophat potential smoothing
Michael Schnieders
Force Field Explorer GUI for Tinker; neighbor lists for nonbonded interactions
Chuanjie Wu
solvation free energy calculations; AMOEBA nucleic acid force field; parameterization tools for Tinker
Justin Xiang
angular overlap and valence bond potential models for transition metals
David Gohara
OpenMP parallelization of energy terms including PME, and parallel neighbor lists
Chao Lu
derivatives of potential energy with respect to lambda for metadynamics and similar methods
Aaron Gordon
enthalpy and entropy estimates as an adjunct to BAR free energy calculation
Zhi Wang
Bennett acceptance ratio (BAR) for free energy calculations
Josh Rackers & Rose Silva
implementation of the HIPPO force field for water and general organic molecules
It is critically important that Tinker’s distributed force field parameter sets exactly reproduce the intent of the original force field authors. We would like to thank Julian Tirado-Rives (OPLS-AA), Alex MacKerell (CHARMM27), Wilfred van Gunsteren (GROMOS), and Adrian Roitberg and Carlos Simmerling (AMBER) for their help in testing Tinker’s results against those given by the authentic programs and parameter sets. Lou Allinger provided updated parameters for MM2 and MM3 on several occasions. His very successful methods provided the original inspiration for the development of Tinker.
Still other workers have devoted considerable time in developing code that will hopefully be incorporated into future Tinker versions; for example, Jim Kress (UFF implementation) and Michael Sheets (numerous code optimizations, thermodynamic integration). Finally, we wish to thank the many users of the Tinker package for their suggestions and comments, praise and criticism, which have resulted in a variety of improvements.