I am currently working on a project looking for anti-freeze protein (AFP) substitutes. I was hoping to get some preliminary data using MD simulations and docking of my AFP substitutes with hexagonal ice (Ih). I have had some trouble finding information online on how to incorporate the hexagonal ice into MD simulations or docking as the 'receptor'. It seems that most labs are using either GROMACS or Hex for their MD simulations. I will post below some of the articles that run MD simulations and docking on AFPs as well as some other relevant papers. Any information would be a huge help!

Articles performing MD simulations and/or docking on AFPs:

• eLife, 4, e05142. doi.org/10.7554/eLife.05142
• Molecular informatics, 35(6-7), 268–277. doi.org/10.1002/minf.201600034
• Microbial cell factories, 16(1), 138. doi.org/10.1186/s12934-017-0737-2

Water model cited in many of the AFP MD simulation papers:

• J. Chem. Phys. 122, 234511 (2005). doi.org/10.1063/1.1931662

Hex user manual:

• https://hex.loria.fr/manual800/hex_manual.pdf