Recent Developments in Amber Biomolecular Simulations

David A. Case; David S. Cerutti; Vinícius Wilian D. Cruzeiro; Thomas A. Darden; Robert E. Duke; Mahdieh Ghazimirsaeed; George M. Giambaşu; Timothy J. Giese; Andreas W. Götz; Julie A. Harris; Koushik Kasavajhala; Tai Sung Lee; Zhen Li; Charles Lin; Jian Liu; Yinglong Miao; Romelia Salomon-Ferrrer; Jana Shen; Ryan Snyder; Jason Swails; Ross C. Walker; Jinan Wang; Xiongwu Wu; Jinzhe Zeng; Thomas E. Cheatham; Daniel R. Roe; Adrian Roitberg; Carlos Simmerling; Darrin M. York; Maria C. Nagan; Kenneth M. Merz

doi:10.1021/acs.jcim.5c01063

Recent Developments in Amber Biomolecular Simulations

David A. Case
, David S. Cerutti
, Vinícius Wilian D. Cruzeiro
, Thomas A. Darden
, Robert E. Duke
, Mahdieh Ghazimirsaeed
, George M. Giambaşu
, Timothy J. Giese
, Andreas W. Götz
, Julie A. Harris
, Koushik Kasavajhala
, Tai Sung Lee
, Zhen Li
, Charles Lin
, Jian Liu
, Yinglong Miao
, Romelia Salomon-Ferrrer
, Jana Shen
, Ryan Snyder
, Jason Swails

Ross C. Walker, Jinan Wang, Xiongwu Wu, Jinzhe Zeng, Thomas E. Cheatham, Daniel R. Roe, Adrian Roitberg, Carlos Simmerling, Darrin M. York, Maria C. Nagan, Kenneth M. Merz

Stony Brook University

Rutgers - The State University of New Jersey, New Brunswick
University of Florida
National Institutes of Health
University of North Carolina at Chapel Hill
Advanced Micro Devices
University of California at San Diego
University of Maryland, Baltimore
Stony Brook University
Michigan State University
Cleveland Clinic Foundation
Cold Start Therapeutics
Peking University
Iambic Therapeutics, Inc.
University of Utah

Research output: Contribution to journal › Article › peer-review

30 Scopus citations

Abstract

Amber is a molecular dynamics (MD) software package first conceived by Peter Kollman, his lab and collaborators to simulate biomolecular systems. The pmemd module is available as a serial version for central processing units (CPUs), NVIDIA and Advanced Micro Devices (AMD) graphics processing unit (GPU) versions as well as Message Passing Interface (MPI) parallel versions. Advanced capabilities include thermodynamic integration, replica exchange MD and accelerated MD methods. A brief update to the software and recently added capabilities is described in this Application Note.

Original language	English
Pages (from-to)	7835-7843
Number of pages	9
Journal	Journal of Chemical Information and Modeling
Volume	65
Issue number	15
DOIs	https://doi.org/10.1021/acs.jcim.5c01063
State	Published - Aug 11 2025

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Case, D. A., Cerutti, D. S., Cruzeiro, V. W. D., Darden, T. A., Duke, R. E., Ghazimirsaeed, M., Giambaşu, G. M., Giese, T. J., Götz, A. W., Harris, J. A., Kasavajhala, K., Lee, T. S., Li, Z., Lin, C., Liu, J., Miao, Y., Salomon-Ferrrer, R., Shen, J., Snyder, R., ... Merz, K. M. (2025). Recent Developments in Amber Biomolecular Simulations. Journal of Chemical Information and Modeling, 65(15), 7835-7843. https://doi.org/10.1021/acs.jcim.5c01063

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title = "Recent Developments in Amber Biomolecular Simulations",

abstract = "Amber is a molecular dynamics (MD) software package first conceived by Peter Kollman, his lab and collaborators to simulate biomolecular systems. The pmemd module is available as a serial version for central processing units (CPUs), NVIDIA and Advanced Micro Devices (AMD) graphics processing unit (GPU) versions as well as Message Passing Interface (MPI) parallel versions. Advanced capabilities include thermodynamic integration, replica exchange MD and accelerated MD methods. A brief update to the software and recently added capabilities is described in this Application Note.",

author = "Case, \{David A.\} and Cerutti, \{David S.\} and Cruzeiro, \{Vin{\'i}cius Wilian D.\} and Darden, \{Thomas A.\} and Duke, \{Robert E.\} and Mahdieh Ghazimirsaeed and Giamba{\c s}u, \{George M.\} and Giese, \{Timothy J.\} and G{\"o}tz, \{Andreas W.\} and Harris, \{Julie A.\} and Koushik Kasavajhala and Lee, \{Tai Sung\} and Zhen Li and Charles Lin and Jian Liu and Yinglong Miao and Romelia Salomon-Ferrrer and Jana Shen and Ryan Snyder and Jason Swails and Walker, \{Ross C.\} and Jinan Wang and Xiongwu Wu and Jinzhe Zeng and Cheatham, \{Thomas E.\} and Roe, \{Daniel R.\} and Adrian Roitberg and Carlos Simmerling and York, \{Darrin M.\} and Nagan, \{Maria C.\} and Merz, \{Kenneth M.\}",

note = "Publisher Copyright: {\textcopyright} 2025 The Authors. Published by American Chemical Society",

year = "2025",

month = aug,

day = "11",

doi = "10.1021/acs.jcim.5c01063",

language = "English",

volume = "65",

pages = "7835--7843",

journal = "Journal of Chemical Information and Modeling",

issn = "1549-9596",

publisher = "American Chemical Society",

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Case, DA, Cerutti, DS, Cruzeiro, VWD, Darden, TA, Duke, RE, Ghazimirsaeed, M, Giambaşu, GM, Giese, TJ, Götz, AW, Harris, JA, Kasavajhala, K, Lee, TS, Li, Z, Lin, C, Liu, J, Miao, Y, Salomon-Ferrrer, R, Shen, J, Snyder, R, Swails, J, Walker, RC, Wang, J, Wu, X, Zeng, J, Cheatham, TE, Roe, DR, Roitberg, A, Simmerling, C, York, DM, Nagan, MC & Merz, KM 2025, 'Recent Developments in Amber Biomolecular Simulations', Journal of Chemical Information and Modeling, vol. 65, no. 15, pp. 7835-7843. https://doi.org/10.1021/acs.jcim.5c01063

TY - JOUR

T1 - Recent Developments in Amber Biomolecular Simulations

AU - Case, David A.

AU - Cerutti, David S.

AU - Cruzeiro, Vinícius Wilian D.

AU - Darden, Thomas A.

AU - Duke, Robert E.

AU - Ghazimirsaeed, Mahdieh

AU - Giambaşu, George M.

AU - Giese, Timothy J.

AU - Götz, Andreas W.

AU - Harris, Julie A.

AU - Kasavajhala, Koushik

AU - Lee, Tai Sung

AU - Li, Zhen

AU - Lin, Charles

AU - Liu, Jian

AU - Miao, Yinglong

AU - Salomon-Ferrrer, Romelia

AU - Shen, Jana

AU - Snyder, Ryan

AU - Swails, Jason

AU - Walker, Ross C.

AU - Wang, Jinan

AU - Wu, Xiongwu

AU - Zeng, Jinzhe

AU - Cheatham, Thomas E.

AU - Roe, Daniel R.

AU - Roitberg, Adrian

AU - Simmerling, Carlos

AU - York, Darrin M.

AU - Nagan, Maria C.

AU - Merz, Kenneth M.

PY - 2025/8/11

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AB - Amber is a molecular dynamics (MD) software package first conceived by Peter Kollman, his lab and collaborators to simulate biomolecular systems. The pmemd module is available as a serial version for central processing units (CPUs), NVIDIA and Advanced Micro Devices (AMD) graphics processing unit (GPU) versions as well as Message Passing Interface (MPI) parallel versions. Advanced capabilities include thermodynamic integration, replica exchange MD and accelerated MD methods. A brief update to the software and recently added capabilities is described in this Application Note.

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EP - 7843

JO - Journal of Chemical Information and Modeling

JF - Journal of Chemical Information and Modeling

IS - 15

ER -

Recent Developments in Amber Biomolecular Simulations

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