Journal
JOURNAL OF CHEMICAL INFORMATION AND MODELING
Volume 58, Issue 10, Pages 2043-2050Publisher
AMER CHEMICAL SOC
DOI: 10.1021/acs.jcim.8b00462
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Funding
- National Institutes of Health [S10OD012346, GM107485, GM62248]
- Blue Waters Sustained-Petascale Computing Project (NSF OCI) [07-25070, PRAC OCI-1515572]
- National Science Foundation [ACI-1548562, OCI-1053575]
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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.
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