MIST: A simple and efficient molecular dynamics abstraction library for integrator development
MIST: A simple and efficient molecular dynamics abstraction library for integrator development
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DOI：
10.1016/j.cpc.2018.10.006
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发表时间：
2019-03-01
影响因子：
6.3
通讯作者：
Leimkuhler, Benedict J.
中科院分区：
文献类型：
--
作者：
Bethune, Iain;Banisch, Ralf;Leimkuhler, Benedict J.
我们目前的MIST，分子集成模拟工具包，一个轻量级的和高效的软件库编写的C++，它提供了一个抽象的接口，常见的分子动力学代码，使快速和便携式开发的新的集成方案的分子动力学。初始版本提供了NAMD-Lite、GROMACS和Amber的插件接口，包括几个标准集成方案、一个约束求解器、使用Langevin Dynamics的温度控制和两个回火方案。我们描述的架构和功能的库和C和Fortran的API，可用于接口额外的MD代码MIST.We显示，一系列的测试系统，MIST介绍了串行，共享内存并行，GPU加速的情况下，可以忽略不计的开销，除了琥珀本地集成直接运行在GPU本身。作为MIST功能的演示，我们描述了一种模拟回火模拟，用于研究真空和详细溶剂条件下丙氨酸-12的自由能格局。程序标题：MIST -分子集成模拟工具包程序文件doi：http://dx.doi.org/10.17632/m2v3483r35.1Licensing规定：BSD 2-条款编程语言：C++（C和Fortran接口）问题的性质：生产分子动力学代码变得越来越复杂，使得难以实现新功能，特别是修改核心MD积分环路的算法。解决方法：MIST为集成器开发人员提供了一个简化的抽象接口，可以通过源代码补丁和库API与各种MD代码进行接口，性能损失最小。限制和不寻常的功能：MIST仅与特定版本的MD代码接口：Amber 14、Gromacs 5.0.2和NAMD-Lite 2.0.3附加评论：MIST可从www.example.com免费获得https://bitbucket.org/extasy-project/mist。(C)2018爱思唯尔B. V.保留所有权利。
We present MIST, the Molecular Integration Simulation Toolkit, a lightweight and efficient software library written in C++ which provides an abstract interface to common molecular dynamics codes, enabling rapid and portable development of new integration schemes for molecular dynamics. The initial release provides plug-in interfaces to NAMD-Lite, GROMACS and Amber, and includes several standard integration schemes, a constraint solver, temperature control using Langevin Dynamics, and two tempering schemes. We describe the architecture and functionality of the library and the C and Fortran APIs which can be used to interface additional MD codes to MIST.We show, for a range of test systems, that MIST introduces negligible overheads for serial, shared memory parallel, and GPU-accelerated cases, except for Amber where the native integrators run directly on the GPU itself. As a demonstration of the capabilities of MIST, we describe a simulated tempering simulation used to study the free energy landscape of Alanine-12 in both vacuum and detailed solvent conditions.Program Title: MIST - Molecular Integration Simulation ToolkitProgram Files doi: http://dx.doi.org/10.17632/m2v3483r35.1Licensing provisions: BSD 2-clauseProgramming language: C++ (C and Fortran interfaces)Nature of problem: Production Molecular Dynamics codes have become increasingly complex, making it difficult to implement new functionality, especially algorithms that modify the core MD integration loop. This places a barrier in the way of new algorithms making their way from theory to implementation.Solution method: MIST provides a simplified abstract interface for integrator developers that may be interfaced via source-code patches and a library API to a variety of MD codes, with minimal loss of performance.Restrictions and unusual features: MIST interfaces only to specific versions of MD codes: Amber 14, Gromacs 5.0.2 and NAMD-Lite 2.0.3Additional comments: MIST is freely available from https://bitbucket.org/extasy-project/mist. (C) 2018 Elsevier B.V. All rights reserved.