Beyond Classical Molecular Dynamics: Developing DL_POLY

DL_POLY是CCP5英国的旗舰代码，是少数几个执行经典分子动力学模拟的国际代码之一。这是一种强大的计算显微镜形式，一个真正的拉普拉斯恶魔，在其中，给定一组特定的原子之间的力，一个人根据牛顿力学跟踪它们不断变化的位置和速度。因此，人们可以在原子水平上分析和理解凝聚态物质的行为。然而，经典的分子动力学有两个主要的局限性，这两个局限性主导了大多数社区对新功能的要求。首先，经典力场的使用限制了模型的准确性，并限制了其适用性--例如，量子效应、键断裂和形成以及电荷转移不包括在内。其次，通过分子动力学可以获得的时间尺度(系统可以被跟踪的时间)太短，无法正确研究化学、物理、材料科学和生物学中很少发生事件的许多现象和过程。我们的目标是解决这两种方法的局限性。我们将在DL_Poly中实现：(A)密度泛函紧束缚(DFTB)，以解决精度和量子效应问题；(B)正向通量采样(FFS)，以实现对罕见事件的模拟，从而解决长时间尺度现象。我们将从项目开始就让社区成员作为顾问和早期用户。计划进行一系列测试应用，以展示新软件的威力：i)检测纳米结构对高度无序的铋氧化物中潜在热电性的电子结构以及局部结构和导电性之间的联系的影响；ii)异质成核，如在纳米粒子的推动下，通过纳米气泡增强癌症治疗中的药物输送(FFS)。这一新功能将在功能材料(EPSRC的优先事项)等领域开辟无数新的应用领域--例如，能源材料、电池材料、纳米材料、铁电、超导体、用于信息和通信技术的热电材料、能源生产存储、运输、医疗保健、国防和消费品。FFS的实施将使用户能够解决各种问题，如晶体成核、蛋白质折叠、孔形成、蛋白质通过孔的转移、磁性纳米结构中的罕见切换、异构化、粗糙表面的润湿、液滴合并和基因开关的翻转。制作的新软件将免费提供给世界各地的学者。这些新功能将确保DL_Poly保持国际竞争力。将向学术界和工业界提供全面的手册、文件和培训。

DL_POLY is a CCP5 flagship UK code, one of a handful of international codes to carry out classical molecular dynamics simulations. These are a powerful form of computational microscope, a real Laplace's demon, in which, given a specified set of forces between atoms, one follows their changing positions and velocities by Newtonian mechanics. One can thus analyse and understand the behaviour of condensed matter at the atomic level. However, classical molecular dynamics has two major limitations which dominate the majority of community requests for new functionality. First, the use of classical force fields limits the accuracy of the model and restricts its applicability -- quantum effects, bond breaking and making and charge transfer are, for example, not included. Secondly, the timescales (the time over which the system can be followed) accessible via molecular dynamics are too short to study properly many phenomena and processes in chemistry, physics, materials science and biology where events occur only rarely. We aim to address both these methodological limitations. We shall implement in DL_POLY: (a) density functional tight binding (DFTB) to address the accuracy and quantum effects problem and (b) forward flux sampling (FFS) to enable simulations of rare events and thus address long timescale phenomena.We shall involve members of the community both as advisers and early users right from the start of the project. A number of test applications are planned to demonstrate the power of the new software: i) examination of the effects of nanostructuring on the electronic structure of potential thermoelectrics and the link between local structure and conductivity in highly disordered bismuth oxides which are among the very best superionic conductors (DFTB) ii) heterogeneous nucleations, such as those promoted by nanoparticles and exploited in enhanced drug delivery by nanobubbles in cancer treatment (FFS). The new functionality will open up a myriad of new applications in areas such as functional materials (an EPSRC priority) -- e.g., energy materials, battery materials, nanomaterials, ferroelectrics, superconductors, thermoelectrics for use in information and communications technology, energy generation storage, transport, healthcare, defence and consumer goods. FFS implementation will enable users to tackle problems as diverse as crystal nucleation, protein folding, pore formation, protein translocation through pores, rare switching in magnetic nanostructures, isomerization, wetting of rough surfaces, droplet coalescence and flipping of genetic switches. The new software produced will be freely available to academics worldwide. The new features will assure that DL_POLY remains internationally competitive. Comprehensive manuals, documentation and training will be made available to both academia and industry.