@article{644527d6a982477e945414bab7d4a923,
title = "GPU-Accelerated Molecular Dynamics and Free Energy Methods in Amber18: Performance Enhancements and New Features",
abstract = "We report progress in graphics processing unit (GPU)-accelerated molecular dynamics and free energy methods in Amber18. Of particular interest is the development of alchemical free energy algorithms, including free energy perturbation and thermodynamic integration methods with support for nonlinear soft-core potential and parameter interpolation transformation pathways. These methods can be used in conjunction with enhanced sampling techniques such as replica exchange, constant-pH molecular dynamics, and new 12-6-4 potentials for metal ions. Additional performance enhancements have been made that enable appreciable speed-up on GPUs relative to the previous software release.",
author = "Lee, {Tai Sung} and Cerutti, {David S.} and Dan Mermelstein and Charles Lin and Scott Legrand and Giese, {Timothy J.} and Adrian Roitberg and Case, {David A.} and Walker, {Ross C.} and York, {Darrin M.}",
note = "Funding Information: The authors are grateful for financial support provided by the National Institutes of Health (GM107485 and GM62248 to D.M.Y.). Computational resources were provided by the Office of Advanced Research Computing (OARC) at Rutgers, The State University of New Jersey, the National Institutes of Health under Grant S10OD012346, the Blue Waters Sustained-Petascale Computing Project (NSF OCI 07-25070 and PRAC OCI-1515572), and the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by the National Science Foundation (ACI-1548562 and OCI-1053575). We gratefully acknowledge the support of the nVidia Corporation with the donation of several Pascal and Volta GPUs and the GPU time on the GPU cluster where the reported benchmark results were performed. Publisher Copyright: {\textcopyright} 2018 American Chemical Society.",
year = "2018",
month = oct,
day = "22",
doi = "10.1021/acs.jcim.8b00462",
language = "English (US)",
volume = "58",
pages = "2043--2050",
journal = "Journal of Chemical Information and Modeling",
issn = "1549-9596",
publisher = "American Chemical Society",
number = "10",
}