分子动力学(MD)模拟是生物分子研究中用于研究动力学的强大计算工具,能量学,以及各种生物系统在原子水平上的相互作用。GROMACS是一种广泛使用的免费和开源的生物分子MD模拟软件,以其效率而闻名。准确度,和广泛的模拟选项。然而,设置的复杂性,跑步,分析不同系统的MD模拟通常会带来重大挑战,需要相当长的时间,努力,和专业知识。这里,我们介绍CHAPERONG,一种自动化蛋白质和蛋白质-配体系统的GROMACSMD模拟管道的工具。CHAPERONg还与GROMACS模块和第三方工具无缝集成,以提供对MD仿真轨迹的全面分析,提供多达20个仿真后处理和轨迹分析。它还简化和自动化已建立的管道,以通过引导的MD伞式采样工作流程进行和分析有偏差的MD模拟。因此,CHAPERONg使初学者GROMACS用户更容易获得MD模拟,同时使专家能够专注于MD模拟工作流程的数据解释和其他可编程程度较低的方面。CHAPERONG是用Bash和Python编写的,源代码可在https://github.com/abeebyekeen/CHAPERONG免费获得。详细的文档和教程可在专用网页上在线访问通过https://abeebyekeen.com/chaperong-online。
Molecular dynamics (MD) simulation is a powerful computational tool used in biomolecular studies to investigate the dynamics, energetics, and interactions of a wide range of biological systems at the atomic level. GROMACS is a widely used free and open-source biomolecular MD simulation software recognized for its efficiency, accuracy, and extensive range of simulation options. However, the complexity of setting up, running, and analyzing MD simulations for diverse systems often poses a significant challenge, requiring considerable time, effort, and expertise. Here, we introduce CHAPERONg, a tool that automates the GROMACS MD simulation pipelines for protein and protein-ligand systems. CHAPERONg also integrates seamlessly with GROMACS modules and third-party tools to provide comprehensive analyses of MD simulation trajectories, offering up to 20 post-simulation processing and trajectory analyses. It also streamlines and automates established pipelines for conducting and analyzing biased MD simulations via the steered MD-umbrella sampling workflow. Thus, CHAPERONg makes MD simulations more accessible to beginner GROMACS users whilst empowering experts to focus on data interpretation and other less programmable aspects of MD simulation workflows. CHAPERONg is written in Bash and Python, and the source code is freely available at https://github.com/abeebyekeen/CHAPERONg. Detailed documentation and tutorials are available online at dedicated web pages accessible via https://abeebyekeen.com/chaperong-online.