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. 2025 Aug 11;65(15):7835-7843.
doi: 10.1021/acs.jcim.5c01063. Epub 2025 Jul 29.

Recent Developments in Amber Biomolecular Simulations

David A Case  1 , David S Cerutti  1 , Vinícius Wilian D Cruzeiro  2 , Thomas A Darden  3 , Robert E Duke  3   4 , Mahdieh Ghazimirsaeed  5 , George M Giambaşu  6 , Timothy J Giese  6 , Andreas W Götz  7 , Julie A Harris  8 , Koushik Kasavajhala  9   10 , Tai-Sung Lee  6 , Zhen Li  11   12 , Charles Lin  13 , Jian Liu  14 , Yinglong Miao  15 , Romelia Salomon-Ferrrer  7 , Jana Shen  8 , Ryan Snyder  6 , Jason Swails  16 , Ross C Walker  7   17 , Jinan Wang  15 , Xiongwu Wu  18 , Jinzhe Zeng  6 , Thomas E Cheatham Iii  19 , Daniel R Roe  20 , Adrian Roitberg  2 , Carlos Simmerling  9   10 , Darrin M York  6 , Maria C Nagan  10 , Kenneth M Merz Jr  11   12
Affiliations

Recent Developments in Amber Biomolecular Simulations

David A Case et al. J Chem Inf Model. .

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.

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Figures

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Historical performance of the Amber GPU accelerated pmemd. The DHFR 4.0 fs NVE benchmark on different GPU models is shown. All benchmarks are executed on a single GPU.
See this image and copyright information in PMC

References

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