Contributors to Amber

This is a partial list of people who have made significant contributions to the Amber code or force field development. Please update this yourself if you have GIT access, or send updates and corrections to case@biomaps.rutgers.edu.

Overall

• Nothing about Amber would have happened without the enthusiastic support and encouragement of Peter Kollman, who led its development for its first quarter century.

Earlier versions

• Paul Weiner wrote the first version of Amber
• Chandra Singh added many things, particularly in MD
• Dave Pearlman added many more things, particularly in free energies
• Jim Caldwell maintained the code, added many features, particularly for polarizable potentials
• Wilfred van Gunsteren contributed the original MD code
• George Seibel, major code reorganization, that became Amber 3A
• Bill Ross handled many code cleanups and updates

Force fields

• Scott Weiner, principal developer of the 1984 and 1986 force fields; other contributions came from D.A. Case, U.C. Singh, C. Ghio, G. Alagona, S. Profeta, Jr., P. Weiner and D.T. Nguyen.
• Wendy Cornell, principal developer of the 1994 protein force field; other contributions came from P. Cieplak, C.I. Bayly, I.R. Gould, K.M. Merz, Jr., D.M. Ferguson, D.C. Spellmeyer, T. Fox, and J.W. Caldwell.
• Yong Duan, principal developer of the 2003 protein force field; other contributions came from C. Wu, S. Chowdhury, M.C. Lee, G. Xiong, W. Zhang, R. Yang, P. Cieplak, R. Luo, T. Lee, J. Caldwell and J. Wang.
• Junmei Wang, principal developer of GAFF (general Amber force field)
• Ray Luo and Lijiang Yang, principal developers of the ff03ua protein force field field; other contributions came from C. Tan, M.J. Hsieh, J. Wang, Y. Duan, P. Cieplak, and J. Caldwell.
• Junmei Wang, principal developer of the ff99 force field, with contributions from P. Cieplak
• Jim Caldwell and Piotr Cieplak, primary developers of the original Amber polarizable force fields
• Carlos Simmerling, principal developer of the "ff99SB" and "ff12SB" force fields, with contributions from V. Hornak, R. Abel, A. Okur, B. Strockbine, A. Roitberg, and James Maier.
• Tom Cheatham has been principal overseer of the nucleic acid force fields
• Yong Duan, principal developer of the "pol12" force fields, with contributions from Junmei Wang, Piotr Cieplak, Ray Luo, Qin Cai, Jun Wang, and Jie Li.

LEaP

• Chris Schafmeister, original author and designer
• David E. Smyth wrote the Widget Creation Library
• Vladimir Romanovski wrote Xraw 3D widget set
• Bill Ross added many things, maintained the code for many years
• Scott Brozell, major code cleanup, feature enhancements
• Wei Zhang, enabled 64 bit support, fixed several bugs. Wei also wrote sleap
• Junmei Wang added code for setup of polarizable potentials

antechamber

• Junmei Wang, principal author and designer
• Chris Bayly developed the AM1-BCC scheme

sander

• Dave Case originally assembled this from earlier pieces, wrote the generalized Born module
• Dave Pearlman contributed much of the NMR restraint code, and the code to parse the "new" prmtop format
• Tom Darden, principal implementor of the PME, extra-points code, and polarizable potential code
• Carlos Simmerling, principal developer of the LES functionality
• Jim Vincent, early work on parallelization
• Tom Cheatham worked to integrate, test and clean sequential and parallel versions
• Mike Crowley made major efforts in parallelization, efficiency, code restructuring and cleanup
• Ross Walker, code cleanup, bugfixes and optimization, added all new QM/MM support, CHARMM support, overhauled GB routines
• Scott Brozell, code cleanup and optimization
• Viktor Hornak contributed the atom-parsing code, based on earlier work by Tom Cheatham
• István Kolossváry contributed the "low-mode" code
• Shuichi Miyamoto wrote the fast settle routines for water
• Vickie Tsui wrote the LCPO routines, worked on early GB
• Alexey Onufriev developed the igb=2, 5 and 7 models
• Hai Nguyen and Carlos Simmerling developed the igb=8 model
• Andreas Svrcek-Seiler developed the cutoff model for Born radii, other GB efficiency improvements
• Thomas Steinbrecher added a new way to set up thermodynamic integration calculations and implemented soft core vdW-potentials
• Stefano Piana suggested vectorization improvements for GB
• Roberto Gomperts and Carlos Sosa implemented many efficiency and parallelization improvements
• Celeste Sagui and Volodymyr Babin helped implement PME for polarizable potentials, and worked on the implementation of the Amoeba force field
• Ray Luo wrote the modules for Poisson-Boltzmann dynamics
• Guanglei Cui contributed the temperature replica-exchange capability, and added some Lagrange mulitplier constraints.
• Dan Roe later extended and cleaned up the temperature-replica exchange code and greatly improved its efficiency.
• Yilin Meng and Jason Swails added the Hamiltonian replica-exchange capability.
• John Mongan added constant pH capabilities; implemented the binary trajectory format; worked on the igb=7 model
• Xiongwu Wu implemented the Self-Guided Molecular/Langevin Dynamics (SGMD/SGLD) simulation algorithm, the Isotropic Periodic Sum (IPS) long-range interaction calculation method, and the EMAP procedures for targeted MD
• Ilyas Yildirim implemented the icfe=2 mixing rules for TI
• Dave Mathews wrote the nudged elastic band implementation, later extended by Christina Bergonzo
• Kim Wong added the empirical valence bond (EVB) capability
• Francesco Paesani and Wei Zhang added the path integral MD code
• Jiri Vanicek contributed the code to do thermodynamic integration with changing masses
• Jian Liu added code to carry out linearized semi-classical initial value representation (LSC-IVR) calculations of time-correlation functions
• Alejandro Crespo, Marcelo Marti and Dario Estrin contributed to the steered MD/Jarzynski code
• Volodymyr Babin added the biased MD and related code
• Yong Duan and Junmei Wang contributed code for polarizable potentials; Jun Wang added support for Thole-based screening
• MengJuei Hsieh and Yong Duan added generic CMAP support

pmemd

• Bob Duke designed and developed this, originally based on the sander module from Amber 6, but by now completely re-written
• Ross Walker and Scott Le Grand wrote the NVIDIA GPU accelerated version
• Jason Swails, Adrian Roitberg, and Ross Walker added replica exchange capability

ptraj and cpptraj

• Tom Cheatham, original author, designer, and person to complain to...
• Michael Crowley cleaned and fixed code
• Vickie Tsui added correlation analysis
• Jed Pitera added support for binning dipoles to visualizing fields
• Dave Case added correlation analysis
• Holger Gohlke implemented the matrix analysis routines
• Stephen Tanner implemented a general purpose clustering facility
• Eric Absgarten implemented significant trajectory I/O performance enhancements.
• Daniel Roe implemented the initial MPI implementation.
• Paul Frybarger and Ross Walker integrated MPI support and performance enhancements.
• Dan Roe designed and implemented cpptraj

Nucleic Acid Builder (NAB)

• Tom Macke designed the language and wrote the basic code
• Dave Case provided the force field routines
• Andreas Svrcek-Seiler contributed in general, and in particular to the GB code
• Russ Brown wrote the second-derivative code
• István Kolossváry contributed the "low-mode" code
• Yannick Bomble worked on normal modes and Langevin modes
• Ray Luo (and his group) contributed the pbsa code
• Tyler Luchko (working with Andriy Kovalenko and Sergey Gusarov) contributed the 3D-RISM code

MM-PBSA and MMPBSA.py

• Irina Massova constructed an original version of these scripts
• Holger Gohlke re-implemented these ideas in Perl
• Ray Luo created the pbsa program used to get Poisson-Boltzmann energetics
• Paul Beroza wrote the molsurf program to compute molecular surface areas
• Jason Swails, T. Dwight McGee, and Bill R. Miller designed and implemented the Python version

QM/MM

• Steve Dixon, main original developer of the Divcon codes
• Bing Wang introduced the key functionality into Amber, and developed the NMR capabilities
• Kennie Merz provided the driving force for this functionality
• Ross Walker and Mike Crowley contributed a major rewrite of the semiempirical codes, integrated QM/MM with PME and GB and vastly improved both speed and accuracy.
• Ross Walker Implemented an initial semi-parallel version of Amber 9's new QM/MM code.
• Kwangho Nam worked on QM/MM integration with Ewald
• Seth Hayik worked on integration of Divcon and Amber
• Adrian Roitberg and Gustavo Seabra worked on the SCC-DFTB implementation

nmode

• Dave Case, original designer and developer
• Jim Caldwell added support for polarizable potentials

Chamber

• Ross Walker, Mike Crowley and Mark Williamson created support for conversion of CHARMM psf and crd to AMBER prmtop and inpcrd files and added support for this functionality to sander and pmemd.