Residue-level coarse-grained (CG) models are one of the most popular tools in biomolecular simulations in the trade-off between modeling accuracy and computational efficiency. The models are useful for simulating slow conformational motions of biomacromolecules as well as large-scale biological phenomena, such as genome-scale chromatin folding or phase-separated membrane-less condensations. For simulating conformational dynamics of multi-domain proteins, the Go model developed by Karanicolas and Books (KB-Go) was modified in Domain motion enhanced model (DoME). In the model, we utilized Motion Tree (MT) to define rigid domains automatically and adjusted the force constants of intra-domain and inter-domain interactions This method was combined with multi-basin models for simulating open-to-closed motions of Adenylate kinase. For large-scale biological systems including many proteins and nucleic acids, we recently implemented several residue-level coarse-grained (CG) models in GENESIS MD software. In the implementations, a single CG particle represents around ten heavy atoms both in proteins and nucleic acids and the structure-based and context-based potentials are efficiently computed in parallel with message-passing-interface (MPI). We will show large-scale CG MD simulations of Herpes simplex virus (HSV) type 2 B-capsid and chromatin models containing more than 1,000 nucleosomes as examples.

Residue-level coarse-grained models in GENESIS for large-scale molecular dynamics simulations

ACS Spring 2022

The official archive and repository for all ACS Meetings & Expositions abstracts and select posters or presentations.