本文翻译自CompChems的文章GROMACS Tutorial: Coarse-Grained Simulations with Martini 3 Force Field 粗粒化模拟与常规的全原子模拟没有本质的区别,(因此本文中一些Gromacs的基本知识会被省略,可以参考另一篇入门文章:GROMACS教程1:Lysozyme),唯一的不同点在于需要先将全原子模型转换成粗粒化模型, 通常的流程如下(下面...
参考资料: Marrink, S. J., Risselada, H. J., Yefimov, S., Tieleman, D. P., & De Vries, A. H. (2007). The MARTINI force field: coarse grained model for biomolecular simulations.The journal of physical chemistry B,111(27), 7812-7824. Monticelli, L., Kandasamy, S. K., Perio...
The coarse-grained Martini force field is widely used in biomolecular simulations. Here we present the refined model, Martini 3 (http://cgmartini.nl), with an improved interaction balance, new bead types and expanded ability to include specific interactions representing, for example, hydrogen bondin...
Automated bonded parameters for Martini 3. Contribute to Martini-Force-Field-Initiative/Bartender development by creating an account on GitHub.
The main focus was on elaborating a realistic CG force field (FF) aimed to reproduce dynamic structural features of protonated PEI chains and, furthermore, to enable massive simulations of DNA-PEI complex formation and condensation. We parametrized CG Martini FF models for PEI in polarizable and ...
Michalowsky, J., Schäfer, L. V., Holm, C. & Smiatek, J. A refined polarizable water model for the coarse-grained MARTINI force field with long-range electrostatic interactions. J. Chem. Phys. 146, 054501 (2017). Thole, B. T. & van Duijnen, P. T. A general population analysis...
粗粒化模拟- Coarse-grained simulation 在各种模拟技术中使用粗粒化(Coarse-grained, CG)模拟进行研究,是一种有效的手段,CG可以增大体系的时间和长度尺度,这是传统的全原子(All-Atom, AA)模型所无法实现的…
在粗粒化模拟的力场广泛使用的是Martini力场,该力场是一种适用于生物分子系统分子动力学模拟的粗粒化力场。Martini的官网:http://cgmartini.nl/index.php,官网中有详细的教程,后面会慢慢讲解。Martini力场为各种生物分子提供参数,包括许多不同的脂质、胆固醇、氨基酸、糖、DNA、富勒烯、胶原蛋白和树突状分子等。下面介...
OLIVES: A Go-like Model for Stabilizing Protein Structure via Hydrogen Bonding Native Contacts in the Martini 3 Coarse-Grained Force Field Kasper B. Pedersen, Luís Borges-Araújo, Amanda D. Stange, Paulo C. T. Souza, Siewert-Jan Marrink, Birgit Schiøtt DOI: 10.26434/chemrxiv-2023-6d61w...
马提尼粗粒度力场（Martini Coarse-Grained Force Field）是生物分子系统分子动力学模拟中广泛应用的一种简化模型。它通过粗粒化技术，实现了对大尺度生物分子系统的研究，相比于全原子模型，其计算速度更快，操作更便捷。Martini力场的官网cgmartini.nl/index.php提供了详细教程，适用于脂质、胆固醇、氨基酸...