Computational Biophysics and Soft Materials
Colina Research Group
Force Field Database

This database is a collection of the molecular models used in some publications of the Colina Research Group at the University of Florida.

Select a molecule by navigating the drop down menu below to obtain information on the force field functional forms and parameters used in published articles. For each model, you may download data files containing all necessary molecular modeling information. If using any of the information provided in this database, please cite the corresponding paper, as listed on the webpage for each model.

Please select an option from the drop down menu to access the force field information:


Monomers:
Molecules:

Contributors
  • Coray Colina - University of Florida
  • Kyle E. Hart - Penn State
  • Lauren J. Abbott - Penn State
  • Michael E. Fortunato - University of Florida
  • Akshay Mathavan - University of Florida
  • Akash Mathavan - University of Florida
  • Farhad Ramezanghorbani - University of Florida
  • Ping Lin - University of Florida
  • Alexander Demidov - University of Florida

Funding
Funding for this project is provided by the U.S. Department of Energy, Office of Science, Basic Energy Sciences, under Award DE-FG02-17ER16362, as part of the Computational Chemical Sciences Program. Funding for this project was initially provided by the National Science Foundation Grant (DMR­0908781 and DMR­1310258).
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Monomers:
Molecules:
Picture Name

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Citation

Please site the following article when using this information:

  • Hart, K. E.; Colina, C. M. “Estimating gas permeability and permselectivity of microporous polymers.” J. Membr. Sci 2014, 468, 259-268

Parameters

A naming scheme is used in this work for each united atom bead. The naming scheme used is:

[element][type][hydrogens]

[element]: the chemical element of the atom

[type]: the chemical environment of the atom,

A = Aromatic, H = Tetrahedral, L = Linear, P = Trigonal Planar, S = Shared Aromatic, K = Ketone

[hydrogens]: the number of bonded hydrogen atoms in the pseudo atom

For example, CH2 is a tetrahedral carbon unit atom bead with two associated hydrogens. An “L” preceding a Linking atom type designates an atom being used in a Polymatic bonding step.



LAMMPS Parameters

Detailed information for the format of LAMMPS data files may be found in the documentation. The specific functional forms used in these data files are the following:

  • Units:
  • Atom Style:
  • Boundary Style:
  • Pair Style:
  • Pair Style Modify:
  • Long Range Coulombic:
  • Bond Style:
  • Angle Style:
  • Dihedral Style:
  • Special Bonds Style:


References
About this data
The structures contained in the adsorbate.tar.gz files are for the following PIMs: carboxyPIM-1, PIM-1, PIM-0, PIM-1cf, PIM-1h, PIM-1n2, PIM-1r7, PIM-1r9, PIM-1tb, PIM-1tms, soPIM-1, soPIM-0, sPIM-0, and sPIM-1. The initial polymer samples were prepared using a generalized simulated polymerization scheme that is available in the Polymatic software package developed by the Colina group. Under the monomers tab you can find the force field, bonding, and original publication information for each of the polymers of intrinsic microporosity (PIMs) simulated. The “unreacted” monomer units of each structure and equilibrated polymer conformation structures are available for download under each PIM’s tab.

Download information
Below is a permanent link to download a collection “freshly cast” and structurally rearranged PIM models. The samples were dynamically restructured in response to the introduction of the adsorbate species listed using a computational sorption-relaxation technique at 300 K. The gas phase adsorption simulations were carried out by iterating between RASPA Monte Carlo and LAMMPS molecular dynamics steps. Extensive details of the procedure can be found in the 2021 Npj. Comput. Mater. publication of D.M. Anstine, D. Tang, D.S. Sholl, and C.M. Colina.
The detailed description of the zipped content can be found in this archive:

Citation

Please site the following article when using this information:

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