Molecular dynamics simulations of protein aggregation: protocols for simulation setup and analysis with Markov state models and transition networks
S. Samantray, W. Schumann, A.-M. Illig, M. Carballo-Pacheco, A. Paul, B. Barz, B. Strodel
The paper provides protocols for setting up and analyzing molecular dynamics simulations of peptide aggregation using GROMACS, including tools for determining oligomer size and deriving Markov state models and transition networks.
bioRxiv · Apr 25, 2020 · PreprintBiophysics