Title: Moltemplate: a coarse-grained molecule builder for LAMMPS
Presenter: Andrew Jewett
Affiliation: Broad Institute
Abstract: The process of building and simulating coarse-grained molecule models is often arduous, and is traditionally done using custom molecular dynamics software, often built from scratch. As a result, the use of such models is arduous and is relatively inaccessible. LAMMPS provides an alternative. LAMMPS is an extremely general, highly customizable, modular, object-oriented alternative platform for molecular dynamics, but the core software does not provide an easy way for users to setup simulations containing molecules.
We have created a new file format for storing (and sharing) molecules and force-fields in LAMMPS. The interpreter which converts these files into LAMMPS data and input files is called moltemplate. Moltemplate files are templates containing all of the text relevant to a particular molecule. Moltemplate can then duplicate it, customize it, and use it as a building-block for constructing larger molecules. Nearly every molecule, molecular assembly, and force-field which LAMMPS can simulate (now and in the future), can be represented in this format. I will show a few (hopefully fun) examples of the diverse systems which can be represented and built with this tool. We hope moltemplate can partially bridge the gap and bring coarse-grained modeling to a wider audience.