Modeling elastic properties of polystyrene through coarse-grained molecular dynamics simulations

This paper presents an extended coarse-grained investigation of the elastic properties of polystyrene. In particular, we employ the well-known MARTINI force field and its modifications to perform extended molecular dynamics simulations at the $\mu$s timescale, which take slow relaxation processes of polystyrene into account, such that the simulations permit analyzing the bulk modulus, the shear modulus, and the Poisson ratio. We show that through the iterative modification of MARTINI force field parameters it turns out to be possible to affect the shear modulus and the bulk modulus of the system, making them closer to those values reported in the experiment.Comment: 29 pages, 8 figure

The Martini Model in Materials Science

The Martini model, a coarse-grained force field initially developed with biomolecular simulations in mind, has found an increasing number of applications in the field of soft materials science. The model's underlying building block principle does not pose restrictions on its application beyond biomolecular systems. Here, the main applications to date of the Martini model in materials science are highlighted, and a perspective for the future developments in this field is given, particularly in light of recent developments such as the new version of the model, Martini 3

MOLECULAR DYNAMICS STUDIES OF BIOMIMETIC MEMBRANES

We have explored the conformational dynamics of the peptide-appended pillar[5]arene (PAP) channel in lipid and block copolymer (BCP) membranes through the use of molecular dynamics (MD) simulations. The novel polymeric structures trans-1,4-polybutadiene (PB), trans-1,4-polyisoprene (PI), and poly-2-methyl-2-oxazoline (PMOXA) were created and parameterized. These structures were then used to build and simulate pure PB12PEO9, PB23 PEO16 , PI12 PEO9 , and PI23PEO16 synthetic BCP membranes. In addition, simulations of the PAP channel inserted into lipid (POPC), PB12 PEO9 , and PB23PEO16 membranes were conducted. Results of simulations containing PAP suggest that the membrane environment can affect the channel dynamics and potentially its diffusive as well as transport characteristics. Next, we began to explore the microscopic structure of block copolymer membranes using coarse-grained methods. We tested original MARTINI force-field parameters by simulating the self-assembly of a POPC lipid bilayer. We then used the MARTINI force-field to build and simulate coarse-grained models of PB12PEO9. The original MARTINI force-field was unable to show the self-assembly of PB 12PEO9 and must therefore be further optimized to observe the desired behavior

The G\=oMartini approach: Revisiting the concept of contact maps and the modelling of protein complexes

We present a review of a series of contact maps for the determination of native interactions in proteins and nucleic acids based on a distance-threshold. Such contact maps are mostly based on physical and chemical construction, and yet they are sensitive to some parameters (e.g. distances or atomic radii) and can neglect some key interactions. Furthermore, we also comment on a new class of contact maps that only requires geometric arguments. The contact map is a necessary ingredient to build a robust G\=oMartini model for proteins and their complexes in the Martini 3 force field. We present the extension of a popular structure-based G\=o-like approach for the study of protein-sugar complexes, and also limitations of this approach are discussed. The G\=oMartini approach was first introduced by Poma et al. J. Chem. Theory Comput. 2017, 13(3), 1366-1374 in Martini 2 force field and recently, it has gained the status of gold-standard for protein simulation undergoing conformational changes in Martini 3 force field. We discuss several studies that have provided support to this approach in the context of the biophysical community.Comment: 19 pages, 3 figure

Martini 3 Coarse-Grained Force Field for Carbohydrates

The Martini 3 force field is a full re-parametrization of the Martini coarse-grained model for biomolecular simulations. Due to the improved interaction balance it allows for more accurate description of condensed phase systems. In the present work we develop a consistent strategy to parametrize carbohydrate molecules accurately within the framework of Martini 3. In particular, we develop a canonical mapping scheme that decomposes arbitrarily large carbohydrates into a limited number of fragments. Bead types for these fragments have been assigned by matching physicochemical properties of mono- and disaccharides. In addition, guidelines for assigning bonds, angles, and dihedrals are developed. These guidelines enable a more accurate description of carbohydrate conformations than in the Martini 2 force field. We show that models obtained with this approach are able to accurately reproduce osmotic pressures of carbohydrate water solutions. Furthermore, we provide evidence that the model differentiates correctly the solubility of the poly-glucoses dextran (water soluble) and cellulose (water insoluble, but soluble in ionic-liquids). Finally, we demonstrate that the new building blocks can be applied to glycolipids, being able to reproduce membrane properties and to induce binding of peripheral membrane proteins. These test cases demonstrate the validity and transferability of our approach

How the Choice of Force-Field Affects the Stability and Self-Assembly Process of Supramolecular CTA Fibers

[Image: see text] In recent years, computational methods have become an essential element of studies focusing on the self-assembly process. Although they provide unique insights, they face challenges, from which two are the most often mentioned in the literature: the temporal and spatial scale of the self-assembly. A less often mentioned issue, but not less important, is the choice of the force-field. The repetitive nature of the supramolecular structure results in many similar interactions. Consequently, even a small deviation in these interactions can lead to significant energy differences in the whole structure. However, studies comparing different force-fields for self-assembling systems are scarce. In this article, we compare molecular dynamics simulations for trifold hydrogen-bonded fibers performed with different force-fields, namely GROMOS, CHARMM General Force Field (CGenFF), CHARMM Drude, General Amber Force-Field (GAFF), Martini, and polarized Martini. Briefly, we tested the force-fields by simulating: (i) spontaneous self-assembly (none form a fiber within 500 ns), (ii) stability of the fiber (observed for CHARMM Drude, GAFF, MartiniP), (iii) dimerization (observed for GROMOS, GAFF, and MartiniP), and (iv) oligomerization (observed for CHARMM Drude and MartiniP). This system shows that knowledge of the force-field behavior regarding interactions in oligomer and larger self-assembled structures is crucial for designing efficient simulation protocols for self-assembling systems

Au Nanoparticles in Lipid Bilayers: a Comparison between Atomistic and Coarse Grained Models

The computational study of the interaction between charged, ligand-protected metal nanoparticles and model lipid membranes has been recently addressed both at atomistic and coarse grained level. Here we compare the performance of three versions of the coarse grained Martini force field at describing the nanoparticle-membrane interaction. The three coarse-grained models differ in terms of treatment of long-range electrostatic interactions and water polarizability. The NP-membrane interaction consists in the transition from a metastable NP- membrane complex, in which the NP is only partially embedded in the membrane, to a configuration in which the NP is anchored to both membrane leaflets. All the three coarse grained models provide a description of the metastable NP-membrane complex that is consistent with that obtained using an atomistic force field. As for the anchoring transition, the polarizable- water Martini correctly describes the molecular mechanisms and the energetics of the transition. The standard version of the Martini model, instead, underestimates the free energy barriers for anchoring and does not completely capture the membrane deformations involved in the transition process

Two decades of Martini:Better beads, broader scope

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 groups of Marrink and Tieleman, the Martini model has over the years been extended as a community effort to the current level of a general-purpose force field. Apart from the obvious benefit of a reduction in computational cost, the popularity of the model is largely due to the systematic yet intuitive building-block approach that underlies the model, as well as the open nature of the development and its continuous validation. The easy implementation in the widely used Gromacs software suite has also been instrumental. Since its conception in 2002, the Martini model underwent a gradual refinement of the bead interactions and a widening scope of applications. In this review, we look back at this development, culminating with the release of the Martini 3 version in 2021. The power of the model is illustrated with key examples of recent important findings in biological and material sciences enabled with Martini, as well as examples from areas where coarse-grained resolution is essential, namely high-throughput applications, systems with large complexity, and simulations approaching the scale of whole cells. This article is categorized under: Software > Molecular Modeling Molecular and Statistical Mechanics > Molecular Dynamics and Monte-Carlo Methods Structure and Mechanism > Computational Materials Science Structure and Mechanism > Computational Biochemistry and Biophysics

Room for improvement in the initial martini 3 parameterization of peptide interactions

Funding Information: We thank T. Cordeiro for bringing to our attention the coiled coil system that motivated part of this study. J.K.S. acknowledges an internship sponsored by Fundação Luso-Americana para o Desenvolvimento through its Study in Portugal Network. M.N.M. thanks Fundação para a Ciência e a Tecnologia, Portugal for fellowship CEECIND/04124/2017 , and for funding project MOSTMICRO-ITQB with references UIDB/04612/2020 and UIDP/04612/2020 . Publisher Copyright: © 2023 The AuthorsThe 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.publishersversionpublishe