Peer-Reviewed Publication
J Chem Inf Model2025;65(15):7835-7843.August 11, 2025Journal Article
Recent Developments in Amber Biomolecular Simulations.
David A Case1, David S Cerutti1, Vinícius Wilian D Cruzeiro2, Thomas A Darden3, Robert E Duke3,4, Mahdieh Ghazimirsaeed5, George M Giambaşu6, Timothy J Giese6, Andreas W Götz7, Julie A Harris8, Koushik Kasavajhala9,10, Tai-Sung Lee6, Zhen Li11,12, Charles Lin13, Jian Liu14, Yinglong Miao15, Romelia Salomon-Ferrrer7, Jana Shen8, Ryan Snyder6, Jason Swails16, Ross C Walker7,17, Jinan Wang15, Xiongwu Wu18, Jinzhe Zeng6, Thomas E Cheatham Iii19, Daniel R Roe20, Adrian Roitberg2, Carlos Simmerling9,10, Darrin M York6, Maria C Nagan10, Kenneth M Merz11,12
1Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, United States.
2Department of Chemistry, The University of Florida, 440 Leigh Hall, Gainesville, Florida 32611-7200, United States.
3National Institute of Environmental Health Sciences, 111 TW Alexander Dr., Durham, North Carolina 27709, United States.
4Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States.
5Advanced Micro Devices Inc., Austin, Texas 78735, United States.
6Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, United States.
7San Diego Supercomputer Center, University of California San Diego, La Jolla, California 92093-0505, United States.
8Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland 21201, United States.
9Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York 11794, United States.
10Department of Chemistry, Stony Brook University, Stony Brook, New York 11794, United States.
11Department of Chemistry and Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824-1322, United States.
12Cleveland Clinic, Lerner Research Institute, 9620 Carnegie Avenue, N Building, Cleveland, Ohio 44106, United States.
13Cold Start Therapeutics, San Diego, California 92126, United States.
14Beijing National Laboratory for Molecular Sciences, Institute of Theoretical and Computational Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China.
15Department of Pharmacology and Computational Medicine Program, University of North Carolina-Chapel Hill, Chapel Hill, North Carolina 27599, United States.
16Iambic Therapeutics, 5627 Oberlin Drive, Suite 120, San Diego, California 92121, United States.
17Department of Chemistry and Biochemistry, University of California-San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States.
18Laboratory of Computational Biology, National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health (NIH), Bethesda, Maryland 20892, United States.
19Department of Medicinal Chemistry, The University of Utah, 30 South 2000 East, Salt Lake City, Utah 84112, United States.
20Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, United States.
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 inc…
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