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 Goetz, Robert C. Harris, Koushik Kasavajhala, Tai‐Sung Lee, Zhen Li, Charles Y. 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, Adrián E. Roitberg, Carlos Simmerling, Darrin M. York, Maria C. Nagan, Kenneth M. Merz
Abstract
High Resolution Image Download MS PowerPoint Slide 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.