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...
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...
Yesylevskyy, S. O., Schäfer, L. V, Sengupta, D. & Marrink, S. J. Polarizable water model for the coarse-grained MARTINI force field. PLoS Comput. Biol. 6, e1000810 (2010). Michalowsky, J., Schäfer, L. V., Holm, C. & Smiatek, J. A refined polarizable water model for...
Automated bonded parameters for Martini 3. Contribute to Martini-Force-Field-Initiative/Bartender development by creating an account on GitHub.
The Martini 3 protein force field is an evolution of its Martini 2 counterpart, aimed at improving many of the shortcomings that had been previously identified. In this mini-review, we first provide a general overview of the model and then focus on the successful advances made in the short ...
The coarse-grained Martini force field is widely used in biomolecular simulations. Here we present the refined model, Martini 3 (), with an improved interaction balance, new bead types and expanded ability to include specific interactions representing, for example, hydrogen bonding and electronic pola...
We ran simulations with the Martini 3 force field6 with the well-depth, ϵ, in the Lennard-Jones potential between all protein beads rescaled by a factor λPP or with ϵ in the Lennard-Jones potential between all protein backbone and water beads rescaled by a factor λPW-BB. We ...
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...
The new version, coined the MARTINI force field, is parametrized in a systematic way, based on the reproduction of partitioning free energies between polar and apolar phases of a large number of chemical compounds. To reproduce the free energies of these chemical building blocks, the number of ...
在Martini 3的上下文中,将2-5个重原子映射到一个珠子中,其中映射原子的数量及其连通性决定了珠子的大小。 其支持信息: 官网的示例: http://cgmartini.nl/index.php/force-field-parameters/particle-definitions 对于芳香烃来说一定要注意的VS虚拟相互作用位点 ...