These are preliminary reports that have not been peer-reviewed. They should not be regarded as conclusive, guide clinical practice/health-related behavior, or be reported in news media as established information. For more information, please see our FAQs.
2 files

Pitfalls of the Martini Model

submitted on 15.05.2019 and posted on 16.05.2019 by Riccardo Alessandri, Paulo C. T. Souza, Sebastian Thallmair, Manuel N. Melo, Alex H. de Vries, Siewert-Jan Marrink

The computational and conceptual simplifications realized by coarse-grain (CG) models make them an 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.


Netherlands Organisation for Scientific Research NWO (Graduate Programme Advanced Materials, No. 022.005.006)

Marie Sklodowka-Curie Actions Individual Fellowship (MicroMod-PSII, grant agreement 748895)


Email Address of Submitting Author


University of Groningen


The Netherlands

ORCID For Submitting Author


Declaration of Conflict of Interest

There are no conflicts to declare.


Read the published paper

in Journal of Chemical Theory and Computation

Logo branding