GenEvaPa: A generic evaporation package for modeling evaporation in molecular dynamics simulations
GenEvaPa: A generic evaporation package for modeling evaporation in molecular dynamics simulations
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DOI：
10.1016/j.cpc.2022.108539
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发表时间：
2022-09-16
影响因子：
6.3
通讯作者：
Faller, Roland
中科院分区：
文献类型：
--
作者：
Harris, Bradley;Liu, Gang-yu;Faller, Roland
这项工作提出了一种新的通用工具，用于模拟蒸发过程，而无需使用Python修改现有的软件。该工具是基于MDAnalysis软件包开发的，该软件包用于导入分子动力学轨迹。然后，该工具将移除溶剂分子并输出新的结构文件，以用于进一步的模拟和分析。此过程设计为通过使用生成的动力学模拟轨迹作为输入文件来迭代。蒸发被设计为随机删除溶剂分子，同时保留溶质周围的溶剂化壳。蒸发速率可以通过MD模拟的长度和动态模拟之间去除的颗粒数量来控制。使用Gromacs套件对该工具的有效性进行了广泛的测试。该工具的优点包括其通用性，简单性和用户友好性，因为不需要对现有软件平台或Gromacs特定工具进行重大修改。节目摘要节目标题：GenEvaPa CPC Library链接到程序文件：https：//doi.org/10.17632/y5c3jnbjvs.1开发者的存储库链接：github .com /bradsharris /GenEvaPa许可条款：GNU通用公共许可证3编程语言：Python >3问题的性质：原子和粗粒度分子动力学模拟中的近似蒸发/干燥过程，同时在感兴趣的溶质周围保持溶剂化壳。以这种方式强制干燥允许研究一系列浓度和自组装相互作用。解决方法：现有分子动力学代码的Python包装器，相对于溶质周围的距离标准随机选择溶剂以保持溶剂化壳。最终结构文件的删除保持了MD源代码的通用适用性，并能够纳入自动循环以研究更长时间的干燥。(c)2022年，任作家。由爱思唯尔公司出版。这是一篇开放获取的文章，获得了CC BY-NC-ND许可证（http：//creativecommons.org/licenses/by-nc-nd/4.0/）。
This work presents a novel general tool for modeling the process of evaporation without the need for modifying existing software using Python. The tool was developed based on the MDAnalysis package, which is used to import a Molecular Dynamics trajectory. The tool then removes solvent molecules and outputs a new structure file to be used for further simulation and analysis. This process is designed to be iterated by using the resulting dynamic simulation trajectory as the input file. The evaporation is designed to randomly delete solvent molecules while preserving solvation shells around solutes. The evaporation rate can be controlled by the length of the MD simulations and the number of particles removed between dynamic simulations. Validity of the tool was tested extensively using the Gromacs suite. Advantages of this tool include its genericness, simplicity and user friendliness, as no significant modification of existing software platform or Gromacs specific tools are needed. Program summary Program title: GenEvaPa CPC Library link to program files: https://doi .org /10 .17632 /y5c3jnbjvs .1 Developer's repository link: github .com /bradsharris /GenEvaPa Licensing provisions: GNU General Public License 3 Programming language: Python >3 Nature of problem: Approximate evaporation/drying processes in atomistic and coarse-grained molecular dynamics simulations while maintaining solvation shells around solute of interest. Forced drying in this manner allows for the study of a range of concentrations and self-assembly interactions. Solution method: A python wrapper for existing molecular dynamics codes that randomly selects solvent for removal relative to a distance criteria around a solute to maintain solvation shells. Removal on final structure files maintains generic applicability for MD source codes and enables incorporation into automated loops to study longer drying. (c) 2022 The Authors. Published by Elsevier B.V. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).