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...
Two different cut-off schemes are applied in the BMW-MARTINI force field: modified BMH potential with switch for BMW-BMW interactions, and Lennard-Jones (LJ) potential with the shift scheme in GROMACS for all other interactions. The switching function is...
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 interac
; For a thorough comparison of different mdp options in combination with the Martini force field, see: ; D.H. de Jong et al., Martini straight: boosting performance using a shorter cutoff and GPUs, submitted. title = Martini ('new' parameters for) NPT run ; TIMESTEP IN MARTINI ; Most ...
The coarse grain Martini force field has been widely used to enhance sampling. In its original implementation, this force field applied a shifted Lennard-Jones potential for the non-bonded van der Waals interactions, to avoid problems related to a relatively short cutoff. Here we investigate the ...
The 2 nm cutoff for domains in -rdd is where a LJ potential with energy minimum distance at 0.55 nm (the OLIVES cutoff) goes to 0, and therefore not important if missed. Basic setup The OLIVES script can be called from the command line. The options of the program can be viewed by ...
the MARTINI force field may not capture the important interactions between atoms in a given molecule. Additionally, because the non-bonded interaction parameters are optimized to free energy data, the temperature dependence of the MARTINI force field is inherently incorrect (seeSection 4.3on challenges...
文章最后还提到了考虑以后二级结构可以发生转变 参考文献: de Jong D H, Singh G, Bennett W F D, et al.Improved parameters for the martini coarse-grained protein force field[J]. Journal of Chemical Theory and Computation, 2012, 9(1): 687-697....
Keeping in mind the difficulty of model-ing of ions already with AA force fields, the CG ion force field is only qualitatively accurate Martini力场的限制: 参数对于固体相并不是那么准确,相比液体相来说固体和气体相显得太稳定 内在熵变会丢失,温度依赖性受到了影响。Martini模型,也许在大多数CG方法中一...
even when large time steps are being used. In practice, once every 在实践中,每十步更新一次就很不错,近邻列表的截断距离与非键合力的47; ten steps works fine with a neighborlist cutoff thatisequal to the 截断距离取为相等,1.2nm48; non-bonded cutoff (1.2nm). However, to improve energy conserv...