Agilio Padua

series of papers by A. Padua, J.N. Canongia Lopes et al. J Phys Chem B (since 2004)

• il.ff: database of force field parameters for ions of several ionic liquids (under construction, compatible with the fftool script to create input files for molecular simulation using the LAMMPS, DL_POLY or GROMACS molecular dynamics codes.

• old.il.ff: database of force field parameters for ions of several ionic liquids (previous format, complete with many ions).

• *.zmat, *.mol, *.xyz: input files for ions.

• topologies: topology files in gromacs format for pyridinium and pyrrolidinium ionic liquids, with refined parameters for better representation of transport properties. Contributed by Vitaly Chaban.

• fftool

• Python

• Packmol

Download the files or else clone the repository (easier to stay updated):

git clone https://github.com/agiliopadua/ilff.git

How to build an initial configuration of a molecular or ionic system.

1. For each molecule, ion or fragment of a material prepare a file with atomic coordinates and/or connectivity (covalent bonds). The formats accepted by this tool are .zmat, .mol or .xyz. Detailed information is available in the fftool page.

2. Use the fftool script to create .xyz files for the molecules in your system and an input file for Packmol. For help type fftool -h. For example, to build a simulation box with 20 ion pairs and a density of 3.0 mol/L do:

    fftool 20 c4c1im.zmat 20 ntf2.zmat --rho 3.0
   

3. Use Packmol with the pack.inp file just created to buid the simulation box (adjust the density if necessary):

    packmol < pack.inp
   

   Atom coordinates will be written to a file simbox.xyz. You can use a molecular viewer such as VMD to look at the .xyz files.

4. Use fftool to build the input files for LAMMPS, DL_POLY or Gromacs containing the force field and the coordinates:

    fftool 20 c4c1im.zmat 20 ntf2.zmat --lammps
   

Information on the force field file format and on more geeral or advanced used is available at the fftool page.

• Packmol: L. Martinez et al. J Comp Chem 30 (2009) 2157, DOI: 10.1002/jcc.21224

• LAMMPS: S. Plimton, J Comp Phys 117 (1995) 1, DOI: 10.1006/jcph.1995.1039

• DL_POLY: I.T. Todorov and W. Smith, Daresbury Lab.

• GROMACS M. Abraham , D. van der Spoel, B. Hess, E. Lindahl, et al.

• IL force field: J.N. Canongia Lopes, A.A.H. Padua et al. J Phys Chem B 108 (2004) 2038, DOI: 10.1021/jp0362133; J Phys Chem B 108 (2004) 11250, DOI: 10.1021/jp0476996; J Phys Chem B 108 (2004) 16893, DOI: 10.1021/jp0476545; J Phys Chem B 110 (2006) 19586, DOI: 10.1021/jp063901o; J Phys Chem B 110 (2008) 5039, DOI: 10.1021/jp800281e; J Phys Chem B 110 (2010) 3592, DOI: 10.1021/jp9120468

• OPLS-AA force field: W.L. Jorgensen et al. JACS 118 (1996) 11225, DOI: 10.1021/ja9621760

• AMBER force field: P. Kollman et al. JACS 117 (1995) 5179, DOI: 10.1021/ja00124a002