How to evaluate the interaction between epoxy and a free surface via metadynamics: a coarse-grained example - dataset

Abstract:from [1] Molecular investigations into polymer-surface interactions are essential for understanding and optimizing the mechanicalbehavior of, e.g., adhesive joints or polymer nanocomposites. In this context, metadynamics provides a powerful tool fordetermining the free energy of a molecular system through Gaussian sampling. While the literature demonstrates thatmetadynamics is well suited for adherend–adhesive systems, there is little discussion on the choice of the metadynamicsparameters and their impact on the resulting free energy. This contribution provides a step-by-step methodology fordetermining the parameters of metadynamics, specifically the Gaussian’s depth, width, and deposition time, as well as theconvergence. To illustrate this process, we utilize a simple coarse-grained system made up of a rigid substrate and eitheran epoxy or hardener molecule. Once we establish the optimal metadynamics parameters, we examine the effects ofnon-bonded polymer-surface interactions, which are modeled using 12-6 Lennard–Jones potentials, on the resulting freeenergy surface. As expected, we find that the distance parameter σps influences both the position and depth of the freeenergy well, while the energy parameter εps only affects the well depth. The methodology outlined here can be appliedto more complex systems, making this article a useful guide for advanced studies on adhesive joints and polymer surfaceinteractions in general. Contact: Maximilian RiesInstitute of Applied MechanicsFriedrich-Alexander-Universität Erlangen-NürnbergEgerlandstr. 591058 Erlangen Software: All MD simulations were performed with LAMMPS [2,3], version: 12 June 2025All Metadynamics simulations used the PLUMED [4,5] library (v2.9.4) License: Creative Commons Attribution 4.0 International Context: Data set supplementing journal paper:[1] M. Ries, "How to evaluate the interaction between epoxy and a free surface via metadynamics: A coarse-grained example" Mathematics and Mechanics of Solids (2026)DOI: 10.1177/10812865261429388 Content: Structure of the data set: 01_metadynamics 01_width results corresponding to Section 3.1 DGEBA simulation folder PACM simulation folder 02_height results corresponding to Section 3.3 DGEBA simulation folder PACM simulation folder 03_eps-sigma results corresponding to Section 3.2 & 3.4 DGEBA simulation folder PACM simulation folder 02_umbrella_sampling results corresponding to Section 3.2 Each simulation folder contains execute_lmp.sh bash file to start lammps/metad runs main.in lammps input file potential_coeff.in file containing force field parameters Standard_Input folder containing pre-equilibrated PACM & DGEBA molecules OUT* output folders, named after main parameters; containing main result files, i.e., tracking collective variables, and all information to assemble the free energy surface References: [1] M. Ries, "How to evaluate the interaction between epoxy and a free surface via metadynamics: A coarse-grained example" Mathematics and Mechanics of Solids (2026)DOI: 10.1177/10812865261429388 [2] S. Plimpton, “Fast parallel algorithms for short-range molecular dynamics,” Journal of computational physics, 1995, 117, 1-19. [3] A. P. Thompson et al., “LAMMPS - a flexible simulation tool for particle-based materials modeling at the atomic, meso, and continuum scales,” Computer Physics Communications, vol. 271, p. 108171, 2022. [4] consortium, TP. Promoting transparency and reproducibility in enhanced molecular simulations. Nat Methods 2019; 16(8): 670–673. [5] Tribello, GA, Bonomi, M, Branduardi, D, et al. PLUMED 2: new feathers for an old bird. Comput Phys Commun 2014; 185(2): 604–613.