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:
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).
Choose a Different Molecular Model:
Provided in this download is the force field information used for the model of this molecule, including:
a LAMMPS data file (.lmps).
Provided under the '(Monomers)' is the zipped folder with the force field information used for the
monomer model of this polymer, including: a LAMMPS data file (.lmps), a PDB file (.pdb),
a picture (.png), and a ChemDraw file (.cdx).
Under the '(Polymers)' is the zipped folder with LAMMPS data files of polymer models built
from the corresponding monomers.
Provided in this download is the force field information used for this coarse-grained model, including:
GROMACS input files (.mdp, .gro, .itp) and a Martini parameter file (.itp).
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
A naming scheme is used in this work for each united atom bead. The naming scheme used is:
[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.
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:
Pair Style Modify:
Long Range Coulombic:
Special Bonds Style:
About this data
The structures contained in the adsorbate.tar.gz files are for the following PIMs:
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.
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.