Two decades of Martini: Better beads, broader scope

SJ Marrink, L Monticelli, MN Melo… - Wiley …, 2023 - Wiley Online Library
The Martini model, a coarse‐grained force field for molecular dynamics simulations, has
been around for nearly two decades. Originally developed for lipid‐based systems by the …

Computational modeling of realistic cell membranes

SJ Marrink, V Corradi, PCT Souza, HI Ingolfsson… - Chemical …, 2019 - ACS Publications
Cell membranes contain a large variety of lipid types and are crowded with proteins,
endowing them with the plasticity needed to fulfill their key roles in cell functioning. The …

Martini 3: a general purpose force field for coarse-grained molecular dynamics

PCT Souza, R Alessandri, J Barnoud, S Thallmair… - Nature …, 2021 - nature.com
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 …

Modeling and simulations of polymers: a roadmap

TE Gartner III, A Jayaraman - Macromolecules, 2019 - ACS Publications
Molecular modeling and simulations are invaluable tools for the polymer science and
engineering community. These computational approaches enable predictions and provide …

A review of advancements in coarse-grained molecular dynamics simulations

SY Joshi, SA Deshmukh - Molecular Simulation, 2021 - Taylor & Francis
Over the last few years, coarse-grained molecular dynamics has emerged as a way to model
large and complex systems in an efficient and inexpensive manner due to its lowered …

Simulation of FUS protein condensates with an adapted coarse-grained model

Z Benayad, S von Bulow, LS Stelzl… - Journal of chemical …, 2020 - ACS Publications
Disordered proteins and nucleic acids can condense into droplets that resemble the
membraneless organelles observed in living cells. MD simulations offer a unique tool to …

Martini 3 coarse‐grained force field: small molecules

R Alessandri, J Barnoud, AS Gertsen… - Advanced Theory …, 2022 - Wiley Online Library
The recent re‐parametrization of the Martini coarse‐grained force field, Martini 3, improved
the accuracy of the model in predicting molecular packing and interactions in molecular …

Martini 3 coarse-grained force field for cholesterol

L Borges-Araújo, AC Borges-Araújo… - Journal of Chemical …, 2023 - ACS Publications
Cholesterol plays a crucial role in biomembranes by regulating various properties, such as
fluidity, rigidity, permeability, and organization of lipid bilayers. The latest version of the …

Theoretical and data-driven approaches for biomolecular condensates

KL Saar, D Qian, LL Good, AS Morgunov… - Chemical …, 2023 - ACS Publications
Biomolecular condensation processes are increasingly recognized as a fundamental
mechanism that living cells use to organize biomolecules in time and space. These …

Pitfalls of the Martini model

R Alessandri, PCT Souza, S Thallmair… - Journal of chemical …, 2019 - ACS Publications
The computational and conceptual simplifications realized by coarse-grain (CG) models
make them a ubiquitous tool in the current computational modeling landscape. Building …