Martini straight: Boosting performance using a shorter cutoff and GPUs
Martini straight: Boosting performance using a shorter cutoff and GPUs
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DOI：
10.1016/j.cpc.2015.09.014
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发表时间：
2016-02-01
影响因子：
6.3
通讯作者：
Marrink, Siewert J.
中科院分区：
文献类型：
--
作者：
de Jong, Djurre H.;Baoukina, Svetlana;Marrink, Siewert J.
在分子动力学模拟中，足够的采样是至关重要的，也是该领域的一个持续挑战。粗粒Martini力场已被广泛用于增强采样。在其最初的实现中，该力场为非键合的货车德瓦尔斯相互作用施加了移位的伦纳-琼斯势，以避免与相对较短的截止相关的问题。在这里，我们调查使用一个直截止的Lennard-Jones潜在的潜在修改器。与Verlet邻居搜索算法一起，修改后的潜力允许使用GPU来加速Gromacs中的计算。我们发现，这种替代的潜力有很小的影响，研究的大部分性质，包括分配自由能，散装液体性质和双层性质。与此同时，能源节约保持在合理的范围内。我们的结论是，新提出的直线截止的方法是一个可行的替代标准的Martini中使用的电位，提供显着的加速，即使在没有GPU。(C)2015 Elsevier B. V.版权所有。
In molecular dynamics simulations, sufficient sampling is of key importance and a continuous challenge in the field. The coarse grain Martini force field has been widely used to enhance sampling. In its original implementation, this force field applied a shifted Lennard-Jones potential for the non-bonded van der Waals interactions, to avoid problems related to a relatively short cutoff. Here we investigate the use of a straight cutoff Lennard-Jones potential with potential modifiers. Together with a Verlet neighbor search algorithm, the modified potential allows the use of GPUs to accelerate the computations in Gromacs. We find that this alternative potential has little influence on most of the properties studied, including partitioning free energies, bulk liquid properties and bilayer properties. At the same time, energy conservation is kept within reasonable bounds. We conclude that the newly proposed straight cutoff approach is a viable alternative to the standard shifted potentials used in Martini, offering significant speedup even in the absence of GPUs. (C) 2015 Elsevier B.V. All rights reserved.