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  • To convert LigParGen output to the .ff needed for fftool - ILMD by arcaian. That man is so helpful
  • To generate the PACKMOL and LAMMPS inputs - fftool
  • To build the gemetry - PACKMOL


Generating the XYZ and FF

Start by heading to LigParGen and building your molecule or inputting in the SMILES string and generating the needed files.

From here, you’ll need to save the GROMACS .top file and the LAMMPS .lmp file

Now you’ll need ILMD and can generate the .ff file as such: -g -l lammps.lmp -o molecule.ff

Generating the LAMMPS Input

You want to follow the instructions over at fftool on github, but the basic process is as follows

  1. Generate the PACKMOL script from the pdb file(s) you’ve just generated. The force field will be read form the PBD file.
    • fftool 100 -b 10
  2. Modify the pack.inp to build your geometry how you want it, using the files specified in the file. Examples are available at the packmol website
  3. Run PACKMOL to generate the box
    • packmol < pack.inp
  4. Run the fftool line again, but specify the MD package to generate your scripts (-l for LAMMPS)
    • fftool 100 molecule.pdb -b 10 -l
  5. Modfy the in.lmp and you’re ready to run! you should only need the in.lmp and data.lmp files to run LAMMPS
    • mpirun -np 4 lmp -pk gpu 1 -sf gpu -in in.lmp