Tinker-HP: a massively parallel molecular dynamics package for multiscale simulations of large complex systems with advanced point dipole polarizable force fields.
Tinker-HP: a massively parallel molecular dynamics package for multiscale simulations of large complex systems with advanced point dipole polarizable force fields.
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DOI：
10.1039/c7sc04531j
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发表时间：
2018-01-28
期刊：
影响因子：
8.4
通讯作者：
Piquemal JP
中科院分区：
文献类型：
--
作者：
Lagardère L;Jolly LH;Lipparini F;Aviat F;Stamm B;Jing ZF;Harger M;Torabifard H;Cisneros GA;Schnieders MJ;Gresh N;Maday Y;Ren PY;Ponder JW;Piquemal JP
Tinker-HP是一款致力于极化分子动力学的大规模并行软件。我们提出修补匠HP，一个大规模的MPI并行包，致力于经典分子动力学（MD）和多尺度模拟，使用先进的可极化力场（PFF），包括分布式多极静电。Tinker-HP是流行的Tinker包代码的演变，保留了其使用的简单性和CPU的参考双精度实现。基于应用数学的跨学科努力，Tinker-HP允许在高达数百万个原子的大型系统上进行长极化MD模拟。我们详细的文件中新开发的大规模并行三维空间分解点偶极子极化模型的扩展，以及他们的耦合到有效的Krylov迭代和非迭代极化求解器。代码的设计允许使用各种计算机系统，从实验室工作站到具有数千个核心的现代千万亿次超级计算机。因此，Tinker-HP提出了第一个高性能可扩展的CPU计算环境，用于开发下一代点偶极PFF和生产模拟。还提供了在多尺度极化自洽QM/MD模拟框架中将Tinker-HP与量子力学（QM）联系起来的策略。该软件的可能性，性能和可扩展性证明通过基准计算使用可极化AMOEBA力场的系统范围从大型水箱的大小和离子液体（非常）大的生物系统，包括几种蛋白质以及完整的卫星烟草花叶病毒和核糖体结构。对于小型系统，Tinker-HP似乎与Tinker的Tinker-OpenMM GPU实现具有竞争力。随着系统规模的增长，Tinker-HP仍然可以运行，这要归功于它对分布式内存的访问，并利用其新算法实现稳定的长时间尺度极化模拟。总体而言，对于最大的系统，观察到单核计算的数千倍加速。扩展目前的CPU实现的修补匠-惠普到其他计算平台进行了讨论。
Tinker-HP is massively parallel software dedicated to polarizable molecular dynamics. We present Tinker-HP, a massively MPI parallel package dedicated to classical molecular dynamics (MD) and to multiscale simulations, using advanced polarizable force fields (PFF) encompassing distributed multipoles electrostatics. Tinker-HP is an evolution of the popular Tinker package code that conserves its simplicity of use and its reference double precision implementation for CPUs. Grounded on interdisciplinary efforts with applied mathematics, Tinker-HP allows for long polarizable MD simulations on large systems up to millions of atoms. We detail in the paper the newly developed extension of massively parallel 3D spatial decomposition to point dipole polarizable models as well as their coupling to efficient Krylov iterative and non-iterative polarization solvers. The design of the code allows the use of various computer systems ranging from laboratory workstations to modern petascale supercomputers with thousands of cores. Tinker-HP proposes therefore the first high-performance scalable CPU computing environment for the development of next generation point dipole PFFs and for production simulations. Strategies linking Tinker-HP to Quantum Mechanics (QM) in the framework of multiscale polarizable self-consistent QM/MD simulations are also provided. The possibilities, performances and scalability of the software are demonstrated via benchmarks calculations using the polarizable AMOEBA force field on systems ranging from large water boxes of increasing size and ionic liquids to (very) large biosystems encompassing several proteins as well as the complete satellite tobacco mosaic virus and ribosome structures. For small systems, Tinker-HP appears to be competitive with the Tinker-OpenMM GPU implementation of Tinker. As the system size grows, Tinker-HP remains operational thanks to its access to distributed memory and takes advantage of its new algorithmic enabling for stable long timescale polarizable simulations. Overall, a several thousand-fold acceleration over a single-core computation is observed for the largest systems. The extension of the present CPU implementation of Tinker-HP to other computational platforms is discussed.
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影响因子：
4.1
作者：
BENNETT, CH
通讯作者：
BENNETT, CH
影响因子：
2.9
作者：
Gordon, MS;Freitag, MA;Stevens, WJ
通讯作者：
Stevens, WJ
影响因子：
4.4
作者：
ESSMANN, U;PERERA, L;PEDERSEN, LG
通讯作者：
PEDERSEN, LG
DOI：
10.1016/s1574-1400(07)03010-1
发表时间：
2007-01-01
期刊：
ANNUAL REPORTS IN COMPUTATIONAL CHEMISTRY, VOL 3
影响因子：
--
作者：
Gordon, Mark S.;Slipchenko, Lyudmilla;Jensen, Jan H.
通讯作者：
Jensen, Jan H.
影响因子：
5.5
作者：
Curutchet, Caries;Munoz-Losa, Aurora;Mennucci, Benedetta
通讯作者：
Mennucci, Benedetta