Contributors to Amber

Information for potential contributors

You are under no obligation whatsoever to provide any bug fixes, patches, or changes to the features, functionality or performance of the Amber project ("Enhancements"); however, if you choose to make your Enhancements available to the Amber development team, then by doing so, you grant the following license: a non-exclusive, royalty-free perpetual license to install, use, modify, prepare derivative works, incorporate into other computer software, distribute, and sublicense such enhancements or derivative works thereof, in binary and source code form.

This means that contributors (or perhaps their employers) still own copyright to their contributions, and can re-use that code at their discretion in other projects. Amber just gets a non-exclusive right to use the code in our project.

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", "ff14SB", "ff19SB" protein force fields, with contributions from V. Hornak, R. Abel, A. Okur, B. Strockbine, A. Roitberg, Carmenza Martinez, James Maier, Koushik Kasavajhala, and Chuan Tian (ff19SB). Phosphorylated and modified amino acids support for "ff14SB" and "ff19SB" were contributed by Lauren Raguette and Kellon Belfon.
Tom Cheatham has been principal overseer of the nucleic acid force fields
Modesto Orozco, Ivan Marchan and Alberto Perez, principal developers of the ParmBSC0 force field for nucleic acids.
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.
Piotr Cieplak, designed and implemented i_resp program for iterative charge fitting for polarizable force fields.
Ross Walker, Age Skjevik, Ben Madej, Knut Teigen, Callum Dickson and Ian Gould principal developers of the AMBER Phospholipid Force Fields (GAFF Lipid, lipid11, lipid14).
Dave Cerutti designed and implemented the ff14ipq protein force field, with contributions from David Case, Bill Swope and Julia Rice.
Saeed Izadi, Ramu Anandakrishnan and Alexey Onufriev developed and implemented OPC water model.
Pengfei Li and Kennie Merz, principle developers of the Li/Merz metal ion force fields in Amber.
G. Andrés Cisneros, Hedieh Torabifard, Yi-Jung Tu, Oleg Starovoytov, and Erik A. Vázquez-Montelongo developed the Ionic Liquids parameters for AMOEBA in pmemd.gem.
Shiji Zhao implemented the py_resp program enabling charge fitting for additive and polarizable force fields.

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
Robin Betz added update ion and solvation methods, bug fixes and checks for numlock.

antechamber

Junmei Wang, principal author and designer
Chris Bayly developed the AM1-BCC scheme
Ross Walker, Dave Case, Mike Crowley and Scott Brozell coupled antechamber with sqm for charge fitting
Ross Walker worked on performance optimizations for AmberTools 15

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 and trajectory post-processing
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 (GB-Neck2 and GB-Neck2nu)
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, implemented the NetCDF restart format and the REMD parts of the NetCDF trajectory format, and enabled post-processing of NetCDF trajectories.
Carlos Simmerling, Asim Okur, and Dan Roe implemented the hybrid and reservoir REMD functionality. Koushik Kasavajhala added support for igb=8.
Yilin Meng, Danial Sabri Dashti, and Jason Swails added the Hamiltonian replica-exchange capability.
John Mongan designed and added constant pH MD in GB solvent; implemented the original NetCDF trajectory format; worked on the igb=7 model
Jason Swails also added support for constant pH MD in explicit solvent, constant pH replica exchange MD (in both implicit and explicit solvent), multi-dimensional replica exchange capabilities, the capability to write force trajectories, and numerous code cleanups and bug fixes.
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 original nudged elastic band (NEB) implementation.
Christina Bergonzo implemented the partial nudged elastic band implementation.
Kim Wong added the empirical valence bond (EVB) capability
Wei Zhang added the path integral MD code
Jiri Vanicek contributed the code to do thermodynamic integration with changing masses
Jian Liu added the code to carry out the linearized semi-classical initial value representation (LSC-IVR) of quantum time-correlation functions. In addition, the Jian Liu research group at Peking University (Zhijun Zhang, Kangyu Yan, Zifei Chen) implemented the unified "middle" thermostat scheme for both MD and PIMD [where both cases (with or without constraints) are considered].
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
Romelia Salomon and Ross Walker wrote the Accelerated Molecular Dynamics (AMD) capabilities.
Yinglong Miao added the Gaussian accelerated MD (GaMD) capability.
InSuk Joung added the charge-relocation code
Andreas Götz, Matthew Clark and Ross Walker developed the QM/MM interface to external quantum chemistry programs
Andreas Götz, and Ross Walker developed the adaptive solvent QM/MM interface
Letif Mones, Andreas Götz, and Ross Walker added support for the adaptive buffered force QM/MM method
Andreas Götz added DFTB3 to built-in QM capabilities
Vinicius Cruzeiro added support for constant Redox Potential MD and constant pH and Redox Potential MD in both implicit and explicit solvent, Redox Potential replica exchange MD, multi-dimensional replica exchange support for pH and Redox Potential dimensions, and bug fixes.
Vinicius Cruzeiro and Delaram Ghoreishi added the possibility of running simulations with energies and forces computed from an external library.
Ali Rahnamoun, Mehmet Cagri Kaymak, Kurt A. O'Hearn and H. Metin Aktulga added ReaxFF/MM support through interfacing with the PureMD code.
Vinicius Cruzeiro, Madushanka Manathunga, Kennie Merz and Andreas Götz integrated sander with QUICK for ab initio QM/MM simulations.
Haixin Wei developed the polarizable Gaussian Multipole (pGM) model.

pmemd

Bob Duke designed and developed this, originally based on the sander module from Amber 6, but by now completely re-written
Jason Swails, Adrian Roitberg, and Ross Walker added the temperature and Hamiltonian replica exchange capability
Jason Swails also added support for the LCPO model (GBSA), the igb=8 model, Amber mask parsing capabilities, constant pH MD (in implicit and explicit solvent), constant pH replica exchange capabilities, multi-dimensional replica exchange, and the capability to write force trajectories.
Dan Roe implemented the NetCDF restart format and the REMD parts of the NetCDF trajectory format.
Romelia Salomon and Ross Walker wrote the Isotropic Periodic Sum (IPS).
Romelia Salomon, Levi Pierce, and Ross Walker wrote the Accelerated Molecular Dynamics (AMD) capabilities.
Ross Walker and Romelia Salomon added the ScaledMD Support.
Joe Kaus and Ross Walker added support for thermodynamic integration.
Vinicius Cruzeiro added support for constant Redox Potential MD and constant pH and Redox Potential MD (implicit and explicit solvent), Redox Potential replica exchange MD, multi-dimensional replica exchange support for pH and Redox Potential dimensions.
Vinicius Cruzeiro and Delaram Ghoreishi added the possibility of running simulations with energies and forces computed from an external library.
Kellon Belfon along with Kevin Hauser, Lucy Fallon and Lauren Raguette added support for CoM angle and CoM dihedral restraints using the nmropt = 1 option.
He Huang added the ability to calculate surface area using a fast pairwise approximation with the gbsa=3 flag. Kellon Belfon added contributions to the pmemd.MPI code to support gbsa=3
Koushik Kasavajhala added reservior remd and hybrid solvent support.
The Jian Liu research group (Haifeng Zheng) integrated the unified "middle" thermostat scheme for MD (with or without constraints).

pmemd.cuda

Romelia Salomon and Ross Walker wrote the Isotropic Periodic Sum (IPS).
Romelia Salomon and Ross Walker wrote the Accelerated Molecular Dynamics (AMD) capabilities.
Ross Walker and Romelia Salomon added the ScaledMD Support.
Jason Swails, Adrian Roitberg, and Ross Walker added replica exchange capability.
Jason Swails also added support for constant pH MD in implicit solvent as well as constant pH replica exchange, multi-dimensional replica exchange, and the capability to write force trajectories.
Perri Needham and Ross Walker developed center of mass restraint support.
Vinicius Cruzeiro added support for constant Redox Potential MD and constant pH and Redox Potential MD (implicit and explicit solvent), Redox Potential replica exchange MD, multi-dimensional replica exchange support for pH and Redox Potential dimensions.
Koushik Kasavajhala added reservior remd and hybrid solvent support.
Kellon Belfon along with Kevin Hauser, Lucy Fallon and Lauren Raguette added support for CoM angle and CoM dihedral restraints using the nmropt=1 option
He Huang, Kellon Belfon, Yuzhang Wang, Lucy Fallon and David Cerutti added the ability to calculate surface area using a fast pairwise approximation with the gbsa=3 flag.
The Jian Liu research group (Haifeng Zheng) integrated the unified "middle" thermostat scheme for MD (with or without constraints).

pmemd.mic

Ross Walker, Perri Needham and Ashraf Bhuiyan developed the Xeon Phi accelerated version of pmemd.

pmemd.gem

Bob Duke, and G. Andrés Cisneros designed and developed this version of pmemd.

mdgx

Dave Cerutti designed and implemented this simulation and parameter fitting program.
Pawel Janowski added shared memory PME capability.

pbsa and pbsa.cuda

Ray Luo original author and designer
Lijiang Yang implemented the spherical harmonic expansion option
Chuck Tan implemented the nonpolar solvent module and optimized pb radii for HF charges, as in the ff94 force field and its modern variants
M.J. Hsieh added the multi-block parallel function and API's
Jun Wang extended the linear fdpb solvers including the iim solver, and also upgraded the dielectric mapping routines
Qin Cai added full nonlinear fdpb solvers, implemented the singularity free algorithm and numerical moleuclar surface routines
Xiang Ye added density function approach to model the molecular surface
Xinping Liu added augmented iim solver for linear fdpb systems
Wesley Smith added membrane system support and periodic boundary support for all linear solvers, added fft solver for periodic system
Li Xiao added charge-view and P3M energy routines for full nonlinear pb systems and developed a new membrane model for channel proteins
Changhao Wang extended and unified all potential/field interpolation/extrapolation routines for both energy and force calculations
Ruxi Qi added GPU supports for the linear PB sovlers
Haixin Wei extended the iim solver by fully utilizing the analytical (density function) molecular surface, and developed GPU-friendly improved Harmonic Average (HA) methods

ptraj

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.
Dan Roe implemented the initial MPI implementation.
Paul Frybarger and Ross Walker integrated MPI support and performance enhancements.

cpptraj

Dan Roe is the designer and lead author.
James Maier contributed code used in the J-coupling calculation.
Jason Swails added the linear interaction energy and volmap actions, the data set running average analysis, and the code used for OpenDX reads/writes.
Jason Swails and Guanglei Cui wrote the SPAM action.
Hannes H. Loeffler contributed code for a new diffusion calculation (stfcdiffusion), and added the density, lipid order, and pairdist actions.
Crystal N. Nguyen, Romelia F. Salomon, Ross Walker, Thomas Young and Michael Gilson added the GIST action.

pytraj

Hai Nguyen is the designer and lead developer.
Dan Roe cpptraj API re-design for pytraj.
Jason Swails contributed to Python API design and building for pytraj

pyMSMT

Pengfei Li, designer and lead developer.
Richa Khatiwada and Pengfei Li added the modified Seminario method into the MCPB.py and CartHess2FC.py programs.

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
Jason Swails added support for variable 1-4 scaling and GB neck models (gb=7 and 8, as implemented in sander)
Ramu Anandakrishnan and Alexey V. Onufriev added the hierarchical charge partitioning approximation.

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
Holger Gohlke and Nadine Homeyer designed and implemented the Free Energy Workflow (FEW)
D'Artagnan Greene added membrane protein-ligand binding supports in the Python version

BAR/PBSA

Edward King added the BAR/PBSA scripts for electronic polarization corrections in alchemical free energy simulations

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 Rewrote the the semiempirical codes, integrating QM/MM with PME and GB
Ross Walker Implemented the initial semi-parallel version
Kwangho Nam worked on QM/MM integration with Ewald
Seth Hayik worked on integration of Divcon and Amber
Adrian Roitberg, Ross Walker and Gustavo Seabra worked on the SCC-DFTB implementation
Tai-Sung Lee wrote the d-orbital code, and many other improvements
Tim Giese worked on SCF convergence
Qiantao Wang developed the PM3-MMX2 model, and worked on energy conservation
Andreas Götz worked on code refactoring, d-oribtals, PM6, disperion and H-bond corrections and CHARMM support
Kyoyeon Park worked on dispersion and H-bond corrections
Wei Lin worked on PM3-MAIS
Ross Walker, Dave Case, Mike Crowley and Scott Brozell developed the stand alone quantum package SQM
Ross Walker implemented sqm optimizations for AmberTools 15
Andreas Götz wrote the DFTB3 code
Vinicius Cruzeiro, Madushanka Manathunga, Kennie Merz and Andreas Götz developed ab initio QM/MM methods with sander and QUICK.

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.
Jason Deckman made significant enhancements and bugfixes to support newer versions of the CHARMM force field.
Robin Betz increased the robustness of the parser to variations in CHARMM parameter and psf files.

paramfit

Ross Walker wrote the original code.
Robin Betz Completely overhauled the code adding gradient support, multi-structure fits, openmp parallelization, genetic algorithm support, improved performance and usability.

emil

Joshua T. Berryman, original designer and developer.
Joe Kaus, made some helpful changes to softcoring in the pmemd kernel.

SEBOMD

Gerald Monard, maintainer, tester, and lead author
Steve L. Dixon, Arjan van der Vaart, Valentin Gogonea, James J. Vincent, Edward N. Brothers, Lance M. Westerhoff and Kenneth M. Merz, Jr wrote the original Divcon99 on which SEBOMD is based
Arjan van der Vaart wrote the original roar/divcon interface
Jennifer Thomas wrote the port to sander
Laurent Teixidor developed the QM Ewald and Particle Mesh Ewald summation
Antoine Marion implemented peptidic corrections and core-core functions (including PIF and MAIS)

QUICK

Kennie Merz, code originally developed in Kennie's group, see QUICK Github site for details.
Madushanka Manathunga, Chi Jin, Kennie Merz, Andy Goetz main developers of the current GPU accelerated version of the code at time of inclusion with AmberTools 21. Lots of code cleanup, new features, performance improvements, including XC quadrature on GPUs and multi-GPU capability, QM/MM features.
Vinicius Cruzeiro, Madushanka Manathunga, Kennie Merz and Andy Goetz developed the QM/MM API and integration with sander.

Miscellaneous

Jason Swails designed and implemented the automatic updating scripts patch_amber.py and its successor, update_amber
Jason Swails designed and implemented the ParmEd topology file editor, parmed.py and its GUI counterpart xparmed.py.
Dave Case, Jason Swails, Tyler Luchko, and Dan Roe made significant contributions and simplifications to the current, overall compilation process.
Pawel Janowski and Dave Cerutti designed and implemented the crystal set-up and analysis routines.
Romain Wolf, Pawel Janowski and Jason Swails designed and implemented the pdb4amber input file preparation tool.
Hai Nguyen rewrote pdb4amber (using ParmEd backend), added visualization module
Saeed Izadi, Boris Aguilar and Alexey Onufriev (with some help from Abhishek Mukhopadhyay) designed and implemented gbnsr6 tool.
Hung Nguyen implemented the small-angle X-ray scattering (SAXS) code.
Hai Nguyen created AmberTools binary build workflow
Hai Nguyen created AmberTools continuous integration and nightly build