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Abstract
The Martini 3 coarse-grain force field has greatly improved upon its predecessor, having already been successfully employed in several applications. Here, we gauge the accuracy of Martini 2 and 3 protein interactions in two types of systems: coiled coil peptide dimers in water and transmembrane peptides. Coiled coil dimers form incorrectly under Martini 2 and not at all under Martini 3. With transmembrane peptides, Martini 3 represents better the membrane thickness–peptide tilt relationship, but shorter peptides do not remain transmembranar. We discuss related observations, and describe mitigation strategies involving either scaling interactions or restraining the system.
Supplementary materials
Title
Supplementary Material for: Room for Improvement in the Initial Martini 3 Parameterization of Peptide Interactions
Description
Table S1: List of simulated systems and duration of each replicate.
Figure S1: Contacts between coiled-coil peptides simulated using Martini 3 with elastic networks.
Figure S2: Membrane thickness away from, and in the vicinity of, WALPs.
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