Facilitating CG Simulations with MAD: The MArtini Database Server

Journal article

Parametrization

Small molecules

Phopholipids

Metabolites

Materials science

Cofactors

Author

Cécile Hilpert, Louis Beranger, Paulo C. T. Souza, Petteri A. Vainikka, Vincent Nieto, Siewert J. Marrink, Luca Monticelli and Guillaume Launay

Doi

https://doi.org/10.1021/acs.jcim.2c01375

Citation (APA 7)

Hilpert, C., Beranger, L., Souza, P. C., Vainikka, P. A., Nieto, V., Marrink, S. J., … & Launay, G. (2023). Facilitating CG simulations with MAD: The MArtini database server. Journal of chemical information and modeling, 63(3), 702-710.

Abstract

The MArtini Database (MAD - https://mad.ibcp.fr) is a web server designed for the sharing of structures and topologies of molecules parametrized with the Martini coarse-grained (CG) force field. MAD can also convert atomistic structures into CG structures and prepare complex systems (including proteins, lipids, etc.) for molecular dynamics (MD) simulations at the CG level. It is dedicated to the generation of input files for Martini 3, the most recent version of this popular CG force field. Specifically, the MAD server currently includes tools to submit or retrieve CG models of a wide range of molecules (lipids, carbohydrates, nanoparticles, etc.), transform atomistic protein structures into CG structures and topologies, with fine control on the process and assemble biomolecules into large systems, and deliver all files necessary to start simulations in the GROMACS MD engine.