MARTINI model

The MARTINI model effectively replaces three to four heavy atoms with a bead, parameterized to reproduce condensed-phase thermodynamic data of small molecules [23]. The MARTINI model has been used to investigate many biological processes, such as lung surfactant collapse [24], nanoparticle permeation in bilayers [25], large domain motion of integral membrane proteins [26], vesicle fusion [27,28], and lateral domain formation in membranes [29]. 

Lipid phase transitions are often slow on the timescale accessible to simulations, such as the gel to liquid-crystalline phase transition. Using the MARTINI model, liquid-crystalline to gel phase transitions and domain formation have been... 

AMBER simulations (in TIP3P explicit solvent model [76]). As such, in terms of speed and efficiency, our GBEMP model underperforms medium-resolution MARTINI model by the factor of about 2 [77] but it can outperform high-resolution PRIMO CG model by the factor of about 2 [36],... 

It is also important that the potential is not so strong that the system can solidify at physiological conditions. For example, the MARTINI water model is known to spontaneously crystallize at physiologically relevant temperatures [17]. This phenomenon is enhanced by the presence of interfaces (e.g., a lipid bilayer surface), and requires the addition of unphysical anlilieeze particles to avoid crystallization. While we note that modifications to the MARTINI water model exist (e.g., adding charge polarization) [41, 42], only the original MARTINI model was tested, since it more closely resembles the model derived via MS IBI (i.e., both... 

Fig. 7 RDFs of the MARTINI model and the atomistic TIP3P model mapped to the CG level for the bulk NVT state...

Fig. 1 Illustration of a buckling simulation using the MARTINI model for DMPC (which uses 10 heads pCT lipid)...

The simple theory put forward by Meinhardt et al. accounts in a unified manner for both ripple phases and raft states in membranes. The prerequisites for the formation of such modulated phases is local phase separation (e.g., in the ripple case, between a liquid and a gel phase, or in the raft case, between a liquid disordered and a liquid ordered phase) and curvature stress in at least one of the two phases (typically the ordered one), resulting, e.g., from a size mismatch between head group and tails. In order to reproduce rippled states or rafts, coarsegrained simulation models must meet these criteria. This is often not the case. For example, the standard version of the popular MARTINI model does not have a ripple phase, because the low-temperature gel phase of saturated phospholipids is until ted. 

Hu M, de Jong DH, Marrink SJ, Desemo M (2013) Gaussian curvature elasticity determined from global shape transformations and local stress distributions a comparative study using the MARTINI model. Farad Discuss 161 365-382... 

Sergi D, Scocchi G, Ortona A Coarse-graining MARTINI model for molecular-dynamics simulations of the wetting properties of graphitic surfaces with non-ionic, long-chain, and T-shaped surfactants, J Chem Phys 137 094904, 2012. 

Marrink, S.J. and Tieleman, D.P. Perspective on the Martini model. Chemical Society... 

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