.png){kind=icon}
返回
BLaDE: A Basic Lambda Dynamics Engine for GPU-Accelerated Molecular Dynamics Free Energy Calculations
.png){kind=icon}
OA
AI
DOI：10.1021/acs.jctc.1c00833.png)
.png){kind=icon}
原文求助.png){kind=icon}
分享.png){kind=icon}
收藏
摘要
En 中文
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.
Keyword:
PARTICLE MESH EWALD
EXPLICIT SOLVENT
DRUG DISCOVERY
EFFICIENT
ACCURATE
SIMULATION
ALGORITHM
PREDICTION
CHARMM
SHAKE
期刊
IF:
5.5
论文数:
1.1W
被引数:
5.4W
机构
引用论文
ISOTHERMAL ISOBARIC MOLECULAR-DYNAMICS SIMULATIONS WITH MONTE-CARLO VOLUME SAMPLING蒙特卡罗体积采样的等温等压分子动力学模拟
PREAI
分享收藏Design of a novel wireless power system using machine learning techniques for drone applications使用机器学习技术设计用于无人机应用的新型无线电源系统
PREAI
分享收藏分享收藏Service‐Learning and Negotiation: Engaging Students in Real‐World Projects That Make a Difference
OAAI
OAAI分享收藏分享收藏Large scale relative protein ligand binding affinities using non-equilibrium alchemy使用非平衡炼金术的大规模相对蛋白质配体结合亲和力.png)
CHEMICAL SCIENCEOAAI
CHEMICAL SCIENCEIF7.4
OAAI分享收藏
查看更多内容