Tool assisted development of glycosaminoglycan (GAG) parameters for the SPICA force field - Detailed Simulation Data
Description
This repository contains video files accompanying a poster presentation at the 6th International Conference on Molecular Simulations (ICMS 2023) & The 61st Annual Meeting of the Biophysical Society of Japan. A copy of the posters will also be included after both conferences close. Abstract excerpt: In this work, we would like to present our progress on the ongoing project of bringing saccharide and glycan parameters to the SPICA (Surface Property fItting Coarse grained model) forcefield. In addition, we would like to make SPICA more accessible. For this purpose, we will be presenting our progress on tools to make working with the forcefield easier, faster, and more compatible. Since GAGs are not present in the SPICA forcefield, parametrisation is necessary. We opted to optimise the interaction parameters by means of fitting to bond and angle distributions (solute bonded parameters), density data (solute - water interactions), radial distribution functions (RDF; solute - solute non-bonded interactions), as well as potential of mean force (solute - lipid bilayer interactions). We also simulated stretching of the oligomer with the adaptive biasing force method to validate the parameters. Here, we present rendered videos of selected trajectories.
Files
Steps to reproduce
The software package used was GROMACS (https://www.gromacs.org/), and LAMMPS (https://www.lammps.org), with the CHARMM36 (https://www.charmm.org/archive/charmm/resources/charmm-force-fields/) forcefield for the all-atom sumilations, and the SPICA (https://spica-ff.org) forcefield for the coarse-grain simulations. Part of the configurations was generated using the CHARMM-GUI online system preparation tool, while the remainder of the prep work and analysis was done with in-house software. Visualisations were created using VMD (https://www.ks.uiuc.edu/Research/vmd/) - an open source molecular dynamics visualisation software, and FFmpeg (https://ffmpeg.org/) multimedia toolkit to assemble the final video files.