Recent Developments in Amber Biomolecular Simulations
Journal of Chemical Information and Modeling vol. 65 p. 7835-7843 DOI: 10.1021/acs.jcim.5c01063 Published: 2025-07-29
David A. Case, David S. Cerutti, Vinícius Wilian D. Cruzeiro, Tom 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 M. Swails, Ross C. Walker, Junmei Wang, Xiongwu Wu, Jinzhe Zeng [ ] , Thomas E. Cheatham, Daniel R. Roe, Adrian E. Roitberg, Carlos Simmerling, Darrin M. York [ ] , Maria C. Nagan, Kenneth M. Merz
<p>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.</p>
