TY - JOUR
T1 - Martini 3 Coarse-Grained Force Field
T2 - Small Molecules
AU - Alessandri, Riccardo
AU - Barnoud, Jonathan
AU - Gertsen, Anders S.
AU - Patmanidis, Ilias
AU - de Vries, Alex H.
AU - Souza, Paulo C.T.
AU - Marrink, Siewert J.
N1 - Funding Information:
R.A. thanks the Dutch Research Council (NWO) (Graduate Programme Advanced Materials, No. 022.005.006) for financial support, and Maria Tsanai for preliminary tests on Martini 3 numerically unstable, T‐bead‐rich systems. J.B. acknowledges funding from the TOP grant from S.J.M. (NWO) and the EPSRC program grant no. EP/P021123/1. This work was partly carried out on the Dutch national e‐infrastructure with the support of SURF Cooperative. A.S.G.'s work has been performed under the Project HPC‐EUROPA3 (INFRAIA‐2016‐1‐730897), with the support of the EC Research Innovation Action under the H2020 Programme; in particular, A.S.G. gratefully acknowledges the support of S.J.M. at the University of Groningen and the computer resources and technical support provided by SURFsara.
Publisher Copyright:
© 2021 The Authors. Advanced Theory and Simulations published by Wiley-VCH GmbH
PY - 2022/1
Y1 - 2022/1
N2 - 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 dynamics simulations. Here, we describe how small molecules can be accurately parametrized within the Martini 3 framework and present a database of validated small molecule models. We pay particular attention to the description of aliphatic and aromatic ring-like structures, which are ubiquitous in small molecules such as solvents and drugs or in building blocks constituting macromolecules such as proteins and synthetic polymers. In Martini 3, ring-like structures are described by models that use higher resolution coarse-grained particles (small and tiny particles). As such, the present database constitutes one of the cornerstones of the calibration of the new Martini 3 small and tiny particle sizes. The models show excellent partitioning behavior and solvent properties. Miscibility trends between different bulk phases are also captured, completing the set of thermodynamic properties considered during the parametrization. We also show how the new bead sizes allow for a good representation of molecular volume, which translates into better structural properties such as stacking distances. We further present design strategies to build Martini 3 models for small molecules of increased complexity.
AB - 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 dynamics simulations. Here, we describe how small molecules can be accurately parametrized within the Martini 3 framework and present a database of validated small molecule models. We pay particular attention to the description of aliphatic and aromatic ring-like structures, which are ubiquitous in small molecules such as solvents and drugs or in building blocks constituting macromolecules such as proteins and synthetic polymers. In Martini 3, ring-like structures are described by models that use higher resolution coarse-grained particles (small and tiny particles). As such, the present database constitutes one of the cornerstones of the calibration of the new Martini 3 small and tiny particle sizes. The models show excellent partitioning behavior and solvent properties. Miscibility trends between different bulk phases are also captured, completing the set of thermodynamic properties considered during the parametrization. We also show how the new bead sizes allow for a good representation of molecular volume, which translates into better structural properties such as stacking distances. We further present design strategies to build Martini 3 models for small molecules of increased complexity.
UR - http://www.scopus.com/inward/record.url?scp=85122152908&partnerID=8YFLogxK
U2 - 10.1002/adts.202100391
DO - 10.1002/adts.202100391
M3 - Article
AN - SCOPUS:85122152908
SN - 2513-0390
VL - 5
JO - Advanced theory and simulations
JF - Advanced theory and simulations
IS - 1
M1 - 2100391
ER -