{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"submitter":["Hayes RL"],"funding":["Division of Chemistry","National Institute of General Medical Sciences","NIGMS NIH HHS"],"pagination":["6799-6807"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC8626863"],"repository":["biostudies-literature"],"omics_type":["Unknown"],"volume":["17(11)"],"pubmed_abstract":["There is an accelerating interest in practical applications of alchemical free energy methods to problems in protein design, constant pH simulations, and especially computer-aided drug design. In the present paper, we describe a basic lambda dynamics engine (BLaDE) that enables alchemical free energy simulations, including multisite λ dynamics (MSλD) simulations, on graphical processor units (GPUs). We find that BLaDE is 5 to 8 times faster than the current GPU implementation of MSλD-based free energy calculations in CHARMM. We also demonstrate that BLaDE running standard molecular dynamics attains a performance competitive with and sometimes exceeding that of the highly optimized OpenMM GPU code. BLaDE is available as a standalone program and through an API in CHARMM."],"journal":["Journal of chemical theory and computation"],"pubmed_title":["BLaDE: A Basic Lambda Dynamics Engine for GPU-Accelerated Molecular Dynamics Free Energy Calculations."],"pmcid":["PMC8626863"],"funding_grant_id":["GM37554","R35 GM130587","GM130587","R01 GM037554","CHE 1506273"],"pubmed_authors":["Buckner J","Brooks CL","Hayes RL"],"additional_accession":[]},"is_claimable":false,"name":"BLaDE: A Basic Lambda Dynamics Engine for GPU-Accelerated Molecular Dynamics Free Energy Calculations.","description":"There is an accelerating interest in practical applications of alchemical free energy methods to problems in protein design, constant pH simulations, and especially computer-aided drug design. In the present paper, we describe a basic lambda dynamics engine (BLaDE) that enables alchemical free energy simulations, including multisite λ dynamics (MSλD) simulations, on graphical processor units (GPUs). We find that BLaDE is 5 to 8 times faster than the current GPU implementation of MSλD-based free energy calculations in CHARMM. We also demonstrate that BLaDE running standard molecular dynamics attains a performance competitive with and sometimes exceeding that of the highly optimized OpenMM GPU code. BLaDE is available as a standalone program and through an API in CHARMM.","dates":{"release":"2021-01-01T00:00:00Z","publication":"2021 Nov","modification":"2025-04-26T16:27:02.113Z","creation":"2025-04-06T15:13:34.834Z"},"accession":"S-EPMC8626863","cross_references":{"pubmed":["34709046"],"doi":["10.1021/acs.jctc.1c00833"]}}