fftool

Agilio Padua

Tool to build force field input files for molecular dynamics.

• fftool.py: python script to build simulation box of molecular or ionic liquids and their mixtures. Requires the Packmol software to create coordinates. Force field files are written in formats suitable for the LAMMPS or DL_POLY molecular dynamics packages.

• Python 2.7

• Packmol

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

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

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

1. For each molecule or ion prepare a file containing a z-matrix (molecule.zmat). See the examples directory and check the Wikipedia entry for "Z-matrix (chemistry)". The fftool.py script determines the connectivity (which atoms are linked by covalent bonds) from the z-matrix. Cyclic molecules require additional connect records to close rings. Improper dihedrals cannot be inferred from connectivity and must be indicated by improper records. After the z-matrix supply the name of a database of force field parameters (database.ff).

2. Use the fftool.py script to create .xyz files for the molecules in your system and an input file for packmol. For help type fftool.py -h. To build a simulation box with 40 ethanol and 300 water molecules and a density of 40.0 mol/L do:

    fftool.py 40 ethanol.zmat 300 spce.zmat --rho 40.0
   

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 simbox.xyz. You can use a molecular viewer such as RasMol or VMD to look at the .xyz files (fftool.py has an option to write IUPAC atomic symbols instead of the atom names from the force field).

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

    fftool.py 40 ethanol.zmat 300 spce.zmat --rho 40.0 --lammps
   

• 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.