Force field for ionic liquids
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.
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.
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.
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
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.
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