Visualization and Molecular Dynamics topologies

In the following you will find the force field files developed by our group. The files are formatted to be used with the GROMACS program (SoftwareX, 2015, 1-2, 19-25).

Additionally, the input molecule is provided in PDB format together with a brief description about the force field parameterization.

Please, cite the related papers if you use the models from this website in your own scientific publications.

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Organic molecules
AP226
AP226 is an alkynylimidazole-based fluorophore namely 5-((4-methoxy)ethynyl)-1-methyl-2-(4-nitrophenyl)-1H-imidazole.
AP292
AP292 is an alkynylimidazole-based fluorophore namely 5-((4-dicyanovinyl)ethynyl)-1-methyl-2-(4-nitrophenyl)-1 H - imidazole.
DPAP
DPAP is a fluorescent molecular rotor namely 4-(diphenylamino)phthalonitrile. The ground-state model proposed has been used to study DPAP in several environments.
Formamide
The model makes use of two virtual sites to mimic the position of the oxygen atom lone-pairs.
N,N-dimethylformamide
Methyl groups in N,N-dimethylformamide are described using a united atom model.
N-methylformamide
The force field has been obtained for both N-methylformamide conformers: cis and trans.
Pyridine
The model is able to describe the interactions both in aqueous solution and in pure pyridine liquid. A virtual site is added to mimic the nitrogen lone pair.
Pyrrole
The model uses atomic charges adjusted applying a fitting procedure to reproduce dipole and quadrupole moments determined by DFT calculations.
Substituted polythiophene
This force field has been generated to study the effect of solvation on the nature of electronic excitation of the molecule.
Zwitterionic Tyrosine
The model has been derived for the zwitterion L-tyrosine obtained by transfer of a proton from the carboxyl to the amino group.
Ions
Calcium ion
Non-bonded model for the calcium ion, developed using the LRR-DE procedure (J. Chem. Theory Comput., 2018, 14 (1), pp 255) using DFT data as reference.
Magnesium ion
Non-bonded model for the magnesium ion, developed using the LRR-DE procedure (J. Chem. Theory Comput., 2018, 14 (1), pp 255) using DFT data as reference.
Nickel ion
Non-bonded model for the nickel ion, developed using the LRR-DE procedure (J. Chem. Theory Comput., 2018, 14 (1), pp 255) using DFT data as reference.
Zinc ion
Non-bonded model for the zinc ion, developed using the LRR-DE procedure (J. Chem. Theory Comput., 2018, 14 (1), pp 255) using DFT data as reference.