Analysis of experimental data with MD simulation
Title: Analysis of experimental data with MD simulation
DNr: NAISS 2024/22-920
Project Type: NAISS Small Compute
Principal Investigator: Lukas Grunewald <>
Affiliation: Uppsala universitet
Duration: 2024-06-27 – 2025-07-01
Classification: 10602


Molecular Dynamics (MD) simulations can be used to complement experimental data and proved to be powerful tools to aid to solve and validate structures and dynamics of proteins. By combining these two methods with experimental data, they can prove previously unexplained changes and behaviors in proteins. For my project, I would use MD simulations to sample different conformational changes of photoreceptor proteins and try to correlate my findings to previous obtained experimental data (time-resolved crystallography data). The resulting data from the MD simulations can then be directly compared to the time-resolved crystallography data, creating and implementing a new method based on our previous studies. The MD simulations have already been performed, but more replicas might have to be calculated. Furthermore, the MD simulations should still be stored on the cluster, before I upload them on a new server when the paper gets accepted.