Dear LAMMPS users,
To facilitate the simulation of systems involving organic molecules using LAMMPS, the Automated Topology Builder (ATB; see atb.uq.edu.au) now provides topology files for all molecules in a LAMMPS compatible format. The LAMMPS files are designed for use with the moltemplate program () that is distributed with LAMMPS in the tools directory. Moltemplate allows forcefield parameters and molecule template files to be combined to build complex systems, enabling a workflow similar to that used to build system topologies in biomolecular MD simulation packages (eg GROMOS, AMBER, CHARMM etc). The ATB provides molecular topology building block files for a wide variety of molecules (> 20,000 and growing) in a variety of formats. Files can be accessed by visiting . Molecules can be found using the internal search tools based on name or chemical formula and selecting from the list of results. Once on the page for the molecule of interest, you should select the tab “Molecular Dynamics (MD) Files”. You will then need to choose “LAMMPS” from the “Format” drop-down box. If a molecule does not exist in the database, it can be added by submitting a new molecule to be processed (instructions in the site FAQ). Instructions on how to use the template files to prepare LAMMPS input data and script files are included in the file headers, and the moltemplate manual will also be helpful.
For example, the files for toluene can be found here: . You will need to register on the site in order to download files. Access to the ATB is provided free for academic (non-commercial) use. Feedback on how these files could be improved is very welcome, as are reports of bugs or problems with the files.
Best regards,
Tom