The LAMMPS Data-File Generator generates LAMMPS data files to perform molecular dynamics simulations with Dreiding or PCFF force field energy terms. 

How to use the tool

1. Upload a file in one of the formats supported by OpenBabel.

• Verify that your input file is correctly formatted according to the atomic coordinate file format used 

2. If the simulation box dimensions are not specified in the file, provide the cell parameters in Angstrom. Works for non-orthogonal systems as well

3. Choose from the force fields supported

4. Provide a bond scale to calculate distance between atoms 

• The tool uses atom radii (scaled) to estimate the bond length between two atoms, so the scaling parameter will impact bond recognition performed using LAMMPS

5. Click Create Data File:  

• The tool will identify the atom types in the structure according to the force field and the bonded parameters such as bonds, angles and dihedrals: types and coefficients for the energy expression used in the force field 

• Non-bonded parameters will be also included in the data file

6. To save the data file, click Download. The browser will open a new tab from where the file can be downloaded. (Please make sure that you have the pop-up blocker disabled for nanoHUB.org)

Researchers should cite this work as follows:

• Carlos Miguel Patiño, Lorena Alzate-Vargas, Chunyu Li, Benjamin P Haley, Alejandro Strachan (2021), "LAMMPS Data-File Generator," https://nanohub.org/resources/struc2lammpsdf. (DOI: 10.21981/QJ7D-XJ02).

  BibTex | EndNote

1. Dreiding
2. Jupyter notebooks
3. LAMMPS
4. molecular dynamics (MD)
5. molecular simulations
6. organic molecular crystals
7. pcff
8. polymers