Gromologist: A GROMACS-oriented utility library for structure and topology manipulation

Abstract

Despite the increasing automation of workflows for the preparation of systems for molecular dynamics simulations, the custom editing of molecular topologies to accommodate non-standard modifications remains a daunting task even for experienced users. To alleviate this issue, we created Gromologist, a utility library that provides the simulation community with a toolbox of primitive operations, as well as useful repetitive procedures identified during years of research. The library has been developed in response to users' feedback, and will continue to grow to include more use cases, thorough automatic testing and support for a broader spectrum of rare features. The program is available at gitlab.com/KomBioMol/gromologist and via Python's pip.