Benchmark for MD simulations of protein complexes
Title: Benchmark for MD simulations of protein complexes
SNIC Project: SNIC 2021/22-662
Project Type: SNIC Small Compute
Principal Investigator: Erik Marklund <>
Affiliation: Uppsala universitet
Duration: 2021-08-31 – 2021-12-01
Classification: 10603


A close collaborator has identified an enzyme with unique complexation dynamics, and we plan to run MD simulations to understand the structural underpinnings for those dynamics. This will require a considerable amount of simulation time so in order to get the best utilisation of the computing resources we will assess the performance of the Tetralith GPU nodes and compare with CPU-only nodes. This will determine which resources we apply for later and how our simulation setup should be designed.