- Below I provide grid files for binding simulations:
- a configuration example to perform Grid-SMD simulations:
- and structure files for glycocalyx systems:
Prof. Koumoutsakos (the corresponding author) posted the solvated glycocalyx structures in the CSE-Lab website. To download them, just go to "Software", then "Simulation", and then "Glycocalyx Structures".
Force field parameters were taken from CHARMM biomolecular force field (see manuscript). However, residue names were changed to comply with NAMD format (PSFgen only accepts residue names with up to four characters). Thus, if you want to run our glycocalyx systems, you should use our re-named force field parameters. You can download the files from this link. The ZIP file includes an example of flow MD simulation and the force field parameters.
- Finally, one of our glycocalyx figures is now included in a Molecular Biology textbook. The figure can be downloaded from here.