Robert Harris

Jamie Smith

Andreas W. Goetz

Jian Liu

Edward King

Holger Gohlke

Peter A. Kollman

Yinglong Miao

David A. Case

H. Metin Aktulga

Kellon Belfon

Joshua T. Berryman

David S. Cerutti

Thomas E. Cheatham III

G. Andrés Cisneros

George Giambasu

Michael K. Gilson

Saeed Izadi

Sergei A. Izmailov

Koushik Kasavajhala

Mehmet C. Kaymak

Andriy Kovalenko

Tom Kurtzman

Taisung Lee

Pengfei Li

Charles Lin

Tyler Luchko

Ido Ben-Shalom

Ray Luo

Scott R. Brozell

Matias Machado

Viet Man

Madushanka Manathunga

Vinícius Wilian D. Cruzeiro

Kenneth M. Merz

Tom A. Darden

Robert E. Duke

Oleg Mikhailovskii

Gérald Monard

Hai Nguyen

Kurt A. O’Hearn

Alexey Onufriev

Scott LeGrand

Feng Pan

Sergio Pantano

Ruxi Qi

Ali Rahnamoun

Daniel R. Roe

Adrian Roitberg

Celeste Sagui

Stephan Schott-Verdugo

Akhil Shajan

Jana Shen

Carlos L. Simmerling

Nikolai R. Skrynnikov

Jason Swails

Ross C. Walker

Jinan Wang

Junmei Wang

Haixin Wei

Xiongwu Wu

Yeyue Xiong

Yi Xue

Darrin M. York

Romain M. Wolf

Shiji Zhao

Amber is the collective name for a suite of programs that allow users to carry out molecular dynamics simulations, particularly on biomolecules. None of the individual programs carries this name, but the various parts work reasonably well together, and provide a powerful framework for many common calculations. The term Amber is also used to refer to the empirical force fields that are implemented here. It should be recognized, however, that the code and force field are separate: several other computer packages have implemented the Amber force fields, and other force fields can be implemented with the Amber programs. Further, the force fields are in the public domain, whereas the codes are distributed under a license agreement. The Amber software suite is divided into two parts: AmberTools22, a collection of freely available programs mostly under the GPL license, and Amber22, which is centered around the pmemd simulation program, and which continues to be licensed as before, under a more restrictive license. Amber22 represents a significant change from the most recent previous version, Amber20. (We have moved to numbering Amber releases by the last two digits of the calendar year, so there are no odd-numbered versions.) Please see https://ambermd.org for an overview of the most important changes. AmberTools is a set of programs for biomolecular simulation and analysis. They are designed to work well with each other, and with the “regular” Amber suite of programs. You can perform many simulation tasks with AmberTools, and you can do more extensive simulations with the combination of AmberTools and Amber itself. Most components of AmberTools are released under the GNU General Public License (GPL). A few components are in the public domain or have other open-source licenses. See the README file for more information.

Amber 2022

Chi Jin

 Madushanka Manathunga

Amber is the collective name for a suite of programs that allow users to carry out molecular dynamics simulations, particularly on biomolecules. None of the individual programs carries this name, but the various parts work reasonably well together, and provide a powerful framework for many common calculations. The term Amber is also used to refer to the empirical force fields that are implemented here. It should be recognized, however, that the code and force field are separate: several other computer packages have implemented the Amber force fields, and other force fields can be implemented with the Amber programs. Further, the force fields are in the public domain, whereas the codes are distributed under a license agreement. The Amber software suite is divided into two parts: AmberTools21, a collection of freely available programs mostly under the GPL license, and Amber20, which is centered around the pmemd simulation program, and which continues to be licensed as before, under a more restrictive license. Amber20 represents a significant change from the most recent previous version, Amber18. (We have moved to numbering Amber releases by the last two digits of the calendar year, so there are no odd-numbered versions.) Please see https://ambermd.org for an overview of the most important changes. AmberTools is a set of programs for biomolecular simulation and analysis. They are designed to work well with each other, and with the “regular” Amber suite of programs. You can perform many simulation tasks with AmberTools, and you can do more extensive simulations with the combination of AmberTools and Amber itself. Most components of AmberTools are released under the GNU General Public License (GPL). A few components are in the public domain or have other open-source licenses. See the README file for more information.

Amber 2021

Julie Harris

Qiang Zhu

Ido Y. Ben-Shalom

Negin Forouzesh

Timothy Giese

Amber is the collective name for a suite of programs that allow users to carry out molecular dynamics simulations, particularly on biomolecules. None of the individual programs carries this name, but the various parts work reasonably well together, and provide a powerful framework for many common calculations.[1, 2] The term Amber is also used to refer to the empirical force fields that are implemented here.[3, 4] It should be recognized, however, that the code and force field are separate: several other computer packages have implemented the Amber force fields, and other force fields can be implemented with the Amber programs. Further, the force fields are in the public domain, whereas the codes are distributed under a license agreement. The Amber software suite is divided into two parts: AmberTools23, a collection of freely available programs mostly under the GPL license, and Amber22, which is centered around the pmemd simulation program, and which continues to be licensed as before, under a more restrictive license. Amber22 represents a significant change from the most recent previous version, Amber20. (We have moved to numbering Amber releases by the last two digits of the calendar year, so there are no odd-numbered versions.) Please see https://ambermd.org for an overview of the most important changes. AmberTools is a set of programs for biomolecular simulation and analysis. They are designed to work well with each other, and with the “regular” Amber suite of programs. You can perform many simulation tasks with AmberTools, and you can do more extensive simulations with the combination of AmberTools and Amber itself. Most components of AmberTools are released under the GNU General Public License (GPL). A few components are in the public domain or have other open-source licenses. See the README file for more information.

Amber 2023

Ellen B. Stechel

Keiji Morokuma

Phillip R. Westmoreland

Anne M. Chaka

Peter T. Cummings

Matthew Neurock

Priya Vashishta

Computational molecular and materials modeling has emerged to deliver solid technological impacts in the chemical, pharmaceutical, and materials industries. It is not the all-predictive science fiction that discouraged early adopters in the 1980s. Rather, it is proving a valuable aid to designing and developing new products and processes. People create, not computers, and these tools give them qualitative relations and quantitative properties that they need to make creative decisions. With detailed analysis and examples from around the world, Applying Molecular and Materials Modeling describes the science, applications, and infrastructures that have proven successful. Computational quantum chemistry, molecular simulations, informatics, desktop graphics, and high-performance computing all play important roles. At the same time, the best technology requires the right practitioners, the right organizational structures, and - most of all - a clearly understood blend of imagination and realism that propels technological advances. This book is itself a powerful tool to help scientists, engineers, and managers understand and take advantage of these advances.

Applying Molecular and Materials Modeling

Peter A. Kollman

Books

Your next favorite book is out there