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BLaDE: A Basic Lambda Dynamics Engine for GPU-Accelerated Molecular Dynamics Free Energy Calculations
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DOI：10.1021/acs.jctc.1c00833.png)
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Abstract
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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 lambda dynamics (MS lambda D) simulations, on graphical processor units (GPUs). We find that BLaDE is 5 to 8 times faster than the current GPU implementation of MS lambda D-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.
Keywords:
PARTICLE MESH EWALD
EXPLICIT SOLVENT
DRUG DISCOVERY
EFFICIENT
ACCURATE
SIMULATION
ALGORITHM
PREDICTION
CHARMM
SHAKE
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5.5
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