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.