Department of Medicinal Chemistry, College of Pharmacy, and The Henry Eyring Center for Theoretical Chemistry, The University of Utah, Salt Lake City, UT 84112-5820, USA; Department of Fundamental Chemistry, Federal University of Pernambuco, Cidade Universitária, Recife, PE 50740-560, Brazil.
Department of Medicinal Chemistry, College of Pharmacy, and The Henry Eyring Center for Theoretical Chemistry, The University of Utah, Salt Lake City, UT 84112-5820, USA; Department of Computational Sciences, Federal University of Juiz de Fora, Juiz de Fora, Brazil.
J Mol Graph Model. 2014 Mar;48:80-6. doi: 10.1016/j.jmgm.2013.12.006. Epub 2013 Dec 25.
A variety of popular molecular dynamics (MD) simulation packages were independently developed in the last decades to reach diverse scientific goals. However, such non-coordinated development of software, force fields, and analysis tools for molecular simulations gave rise to an array of software formats and arbitrary conventions for routine preparation and analysis of simulation input and output data. Different formats and/or parameter definitions are used at each stage of the modeling process despite largely contain redundant information between alternative software tools. Such Babel of languages that cannot be easily and univocally translated one into another poses one of the major technical obstacles to the preparation, translation, and comparison of molecular simulation data that users face on a daily basis. Here, we present the MDWiZ platform, a freely accessed online portal designed to aid the fast and reliable preparation and conversion of file formats that allows researchers to reproduce or generate data from MD simulations using different setups, including force fields and models with different underlying potential forms. The general structure of MDWiZ is presented, the features of version 1.0 are detailed, and an extensive validation based on GROMACS to LAMMPS conversion is presented. We believe that MDWiZ will be largely useful to the molecular dynamics community. Such fast format and force field exchange for a given system allows tailoring the chosen system to a given computer platform and/or taking advantage of a specific capabilities offered by different software engines.
在过去的几十年中，各种流行的分子动力学（MD）模拟软件包被独立开发出来，以达到不同的科学目标。然而，这种软件、力场和分子模拟分析工具的非协调发展，导致了一系列的软件格式和常规准备及分析模拟输入和输出数据的任意约定。尽管不同的软件工具之间存在大量冗余信息，但在建模过程的每个阶段都使用不同的格式和/或参数定义。这种语言的混乱，使得分子模拟数据的准备、翻译和比较成为用户日常面临的主要技术障碍之一。在这里，我们提出了 MDWiZ 平台，这是一个免费访问的在线门户，旨在帮助快速可靠地准备和转换文件格式，使研究人员能够使用不同的设置（包括力场和具有不同潜在形式的模型）重复或生成 MD 模拟数据。介绍了 MDWiZ 的总体结构，详细说明了 1.0 版本的特点，并基于 GROMACS 到 LAMMPS 的转换进行了广泛的验证。我们相信 MDWiZ 将对分子动力学界有很大的帮助。对于给定的系统，这种快速的格式和力场交换允许将所选系统定制到给定的计算机平台，并/或利用不同软件引擎提供的特定功能。
