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Alexey Anikeenko edited this page Oct 5, 2017 · 1 revision

ZIF-8 GROMACS MD files

This repository contains files for molecular dynamics simulation of ZIF-8 metal-organic framework with embedded guest molecules. It accompanies the study of CO2 and N2 gas adsorption in ZIF-8 MOF with embedded TEMPO nitroxide radicals [Sheveleva2017].

Features

  • topology files for GROMACS molecular dynamics package
  • optional topology generator for ZIF-8 supercells with support of periodic boundary conditions
  • modular topology organization: interaction parameters are decoupled from topological structure
  • several ZIF-8 force fields from the literature are implemented
  • each ligand and Zn atom is assigned its own residue number, which is useful for visualization
  • template directory for the simulation of ZIF-8's 2x2x2 supercell with guest molecules, fully automated by the use of Makefiles and symbolic links

Citation

[Sheveleva2017] A.M. Sheveleva, A.V. Anikeenko, A.S. Poryvaev, D.L. Kuzmina, I.K. Shundrina, D.I. Kolokolov, A.G. Stepanov, M.V. Fedin, Probing Gas Adsorption in Metal–Organic Framework ZIF-8 by EPR of Embedded Nitroxides, J. Phys. Chem. C. 121 (2017) 19880–19886. doi:10.1021/acs.jpcc.7b06884.
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