TianCheng Cluster Solution 23.0.0 安装指南(高性能计算中心) 02 鲲鹏GPU生态应用GROMACS简介 分子动力学模拟(molecular dynamics simulation,MD)是时下最广泛为人采用的计算庞大复杂系统的方法,自1970年起,由于分子模拟的发展迅速,人们系统地建立了许多适用于生化分子体系、聚合物、金属与非金属材料的力场,使得计算复杂...
参考资料: 1.Rawat R, Kant K, Kumar A, et al. HeroMDAnalysis: an automagical tool for GROMACS-based molecular dynamics simulation analysis[J]. Future Medicinal Chemistry, 2021, 13(05): 447-456. 2.https://heromdanalysis.wordpress.com/user-manual-2/ 版权信息 本文系AIDD Pro接受的外部投稿,...
To use multiple GPUs for a single simulation, GROMACS assigns the PME force calculation to a single dedicated GPU. It decomposes the non-bonded and bonded force calculations across the remaining GPUs. A single MPI task will control each GPU: these are called PME tasks and Particle-Particle (PP...
These tutorials are designed as introductory material into using theGROMACSsimulation package. GROMACS is free, open-source software, and has consistently been one of the fastest (if notthefastest) molecular dynamics codes available. 这些教程被设计成使用 GROMACS 模拟包的入门材料。GROMACS 是免费的,开源...
In the molecular dynamics simulation, Gromacs does not work alone. Gromacs interact with pymol and Grace. Pymol is an application to visualize molecule structure and Grace is an application in Linux to display graphs. Both applications will support analysis of molecular dynamics simulation.Astuti, ...
2. 理论基础 我们通常认为的无偏分子动力学模拟（unbias molecular dynamics simulation）和物理化学里面描述...
重复文献Classical molecular dynamics simulation of microwave heating of liquids中对于TIP4P水介电常数的计算 很多人刚开始做gromacs都是从重复文献开始,但是gromacs输入文件输出文件参数复杂,对于新手很不友好,需要弄清处理各个文件的意义,才能正确的使用gromacs,所以在此具体地展示如何根据文献中的参数对Gromacs的不同文件...
1.Rawat R, Kant K, Kumar A, et al. HeroMDAnalysis: an automagical tool for GROMACS-based molecular dynamics simulation analysis[J]. Future Medicinal Chemistry, 2021, 13(05): 447-456. 2.https://heromdanalysis.wordpress.com/user-manual-2/ ...
根据Gromacs官网的第一个教程：Introduction to Molecular Dynamics: Simulation of Lysozyme in Water 在用...
OPEPYesModels for protein folding; polymerization research; structure prediction of peptides and small proteins; and simulation of the role of fluid dynamics in protein relaxation and peptide aggregation.http://www-lbt.ibpc.fr/ CHARMMNoA widely recognized and applied molecular dynamics simulation program...