References

• Watkins, Edward K., and William L. Jorgensen. “Perfluoroalkanes: Conformational Analysis and Liquid-State Properties from Ab Initio and Monte Carlo Calculations.” The Journal of Physical Chemistry A 105, no. 16 (April 1, 2001): 4118–25. https://doi.org/10.1021/jp004071w.
• Siu, Shirley W. I., Kristyna Pluhackova, and Rainer A. Böckmann. “Optimization of the OPLS-AA Force Field for Long Hydrocarbons.” Journal of Chemical Theory and Computation 8, no. 4 (April 10, 2012): 1459–70. https://doi.org/10.1021/ct200908r.
• Byutner, Oleksiy G., and Grant D. Smith. “Quantum Chemistry Based Force Field for Simulations of Poly(Vinylidene Fluoride).” Macromolecules 33, no. 11 (May 1, 2000): 4264–70. https://doi.org/10.1021/ma9918295.
• Sahihi, Mehdi, Andres Jaramillo-Botero, William A. Goddard, and Fahmi Bedoui. “Interfacial Interactions in a Model Composite Material: Insights into α → β Phase Transition of the Magnetite Reinforced Poly(Vinylidene Fluoride) Systems by All-Atom Molecular Dynamics Simulation.” The Journal of Physical Chemistry C 125, no. 39 (October 7, 2021): 21635–44. https://doi.org/10.1021/acs.jpcc.1c05894.

How to use

Download the present directory to your working directory (git clone ...). Then gmx x2top -ff pvdf-cnt.
Before applying gmx x2top on CNT configs (.pdb or .gro), change the atomtypes C and H in those configs to CJ and HJ respectively.
Also, after generating the topology file with x2top, change the function type in the [dihedrals] section to 9 for PVDF and 3 for CNT.

Utilities

The scripts. You will find what they do and how to use them within them - as comments.