Dresden 2020 – scientific programme

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BP: Fachverband Biologische Physik

BP 19: Poster VII

BP 19.15: Poster

Tuesday, March 17, 2020, 14:00–16:00, P2/3OG

Targeted Molecular Dynamics Calculations of Free Energy Profiles of Gramicidin A Using a Nonequilibrium Friction Correction — •Miriam Jäger, Gerhard Stock, and Steffen Wolf — Albert-Ludwigs- Universität Freiburg

Standard unbiased molecular dynamics (MD) simulations are impractical to sample rare events due to their high computational costs. An economic approach to simulate such processes are biased MD simulations. We here use targeted MD simulations, which apply a moving distance constraint along some prechosen reaction coordinate to enforce rare transitions. Free energy profiles can be calculated on the fly from such simulations by dissipation-corrected targeted MD, which combines a second-order cumulant expansion of Jarzynski's equality with an interpretation within the framework of Langevin equations of motion [1]. We here applied dissipation-corrected targeted MD to potassium diffusion through ion channels, using the Gramicidin A channel as a test system. Performing a non-equilibrium principal component analysis on backbone dihedral angles to separate different protein conformations appearing during the transfer, we find that the dissipation-corrected free energy profiles correspond well to barriers predicted by other methods. Further, the friction profiles give insight into ion-protein and ion-water molecule interactions.

[1] S. Wolf and G. Stock, Targeted molecular dynamics calculations of free energy profiles using a nonequilibrium friction correction, J. Chem. Theory Comput. 14, 6175 (2018).