Pitfalls of the Martini Model

Abstract

The computational and conceptual simplifications realized by coarse-grain (CG) models make them a ubiquitous tool in the current computational modeling landscape. Building block based CG models, such as the Martini model, possess the key advantage of allowing for a broad range of applications without the need to reparametrize the force field each time. However, there are certain inherent limitations to this approach, which we investigate in detail in this work. We first study the consequences of the absence of specific cross Lennard-Jones parameters between different particle sizes. We show that this lack may lead to artificially high free energy barriers in dimerization profiles. We then look at the effect of deviating too far from the standard bonded parameters, both in terms of solute partitioning behavior and solvent properties. Moreover, we show that too weak bonded force constants entail the risk of artificially inducing clustering, which has to be taken into account when designing elastic network models for proteins. These results have implications for the current use of the Martini CG model and provide clear directions for the reparametrization of the Martini model. Moreover, our findings are generally relevant for the parametrization of any other building block based force field.

Molecular dynamics simulations in photosynthesis

“…In addition, the time scale of the simulations does not correspond to real time anymore but is faster by a factor of approximately 3-10 due to the smoothened energy landscape (Marrink et al 2007). Another limitation is the introduction of artificial energy barriers upon dimerization of molecules because one CG water bead represents multiple water molecules (Alessandri et al 2019). Moreover, the bond lengths and the bonded force constants should remain in the range for which the CG FF was parametrized.…”

“…Moreover, the bond lengths and the bonded force constants should remain in the range for which the CG FF was parametrized. Too short bond lengths or too weak force constants can artificially increase the non-bonded interactions (Alessandri et al 2019).…”

Martini coarse-grained models of imidazolium-based ionic liquids: from nanostructural organization to liquid–liquid extraction

“…Currently, only three classes of ILs models were developed for Martini 2.2, with the studies focused on pure IL, aqueous biphasic mixtures 35,36 and interactions with membranes. 37 Recently a number of limitations of the current version 2.2 of the Martini model have been reviewed, 31,38 which paved the way for developing a new version, Martini 3.0.…”

Resolving Donor–Acceptor Interfaces and Charge Carrier Energy Levels of Organic Semiconductors with Polar Side Chains

“…[61]. The PTEG‐1 model uses the latest EG Martini parameters [ 62 ] which are the most transferable EG parameters within the current version of the Martini force field (EG notably making for a difficult modeling case in Martini partly because it requires a three‐to‐one atoms‐to‐bead mapping [ 63 ] ). The Martini C 60 model was developed in ref.…”

“…© 2020 The Authors. Published by Wiley-VCH GmbH mapping [63] ). The Martini C 60 model was developed in ref.…”