Input files to evaluate properties of organic solids using molecular simulation. For the simulations we use GROMACS and some Python scripts in this repository. The scripts are adapted to some of the CPU clusters we have access to, so will need to be adapted by anyone trying to reproduce parts of this work.
A paper about this work has been published:
- Lisa Schmidt, David van der Spoel and Marie-Madeleine Walz Probing phase transitions in organic crystals using atomistic MD simulations The paper is available under open access from ACS Phys Chem Au.
A paper about peptide crystals has been published as well:
- A. Najla Hosseini and David van der Spoel Simulations of Amyloid-forming Peptides in the Crystal State The paper is available under open access from The Protein Journal
Just for fun we tried simulating peptide crystals using the Martini force field as well.
- A. Najla Hosseini and David van der Spoel Martini on the Rocks: Can a Coarse-Grained Force Field Model Amyloid Peptide Crystals? - J. Phys. Chem. Lett.