Dialogues in the MIDST

Workshop in the MIDST of How to Make the Best of Your μs-long MD Trajectories

Sabanci University, Istanbul, Turkey

Wednesday, March 23, 2022


This one-day workshop is to be delivered by Canan Atilgan from Sabanci University. The morning session will be devoted to the theory of what type of information can be extracted from MD simulations, with special focus on microsecond and longer time scale trajectories that can now be obtained with modest computational resources. Particular attention will be given to how to decide on the proper length and the number of replicates of simulations to run depending on the research problem being investigated. We will then discuss the type of information that can be gained from standard analyses such as RMSF, RMSD, modes, etc. Next, we will go beyond these, to discuss the type of information that may be gained from hydrogen bond lifetimes, SASA tracking, network analyses to detect allostery, cryptic sites and other out-of-the-ordinary properties. The afternoon will be devoted to a hands-on session on RMSF, RMSD, modal analyses, h-bond barcode graphs and their lifetime comparison, dynamical changes in SASA, community detection.