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05.05.21 - Matthias Post "Deviations from Stokes friction in MD pulling simulations of molecular systems"

Matthias Post, Biomolecular Dynamics, University Freiburg
When May 05, 2021
from 04:00 PM to 05:15 PM
Contact Name
Contact Phone 203-97666
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Deviations from Stokes friction in MD pulling simulations of molecular systems

The modeling of biomolecular systems from MD simulations faces the well-known problem of sampling long time transitions. A way to circumvent this problem is to constrain the reaction coordinate to enforce these transitions, called targeted molecular dynamics.[1] While we previously showed that despite this bias the free energy landscape can readily be recovered,[2] we now introduce an analysis framework[3] which is able to also measure the friction to give a full, dynamical picture of these systems, e.g. via a Langevin equation.
We present the application of the method to different non-equilibrium processes, resulting in position and velocity dependent frictional forces. By varying the pulling velocity, these simulations show that there are significant deviations from a simple Stokes friction model. We study several systems, including a Lennard-Jones fluid, NaCl in water, alkane-based lubricants[4] and small peptides. We will discuss these observations by studying the validity of the method, in particular the influence of the constraint to the measured friction.
[1] Schlitter et al., Mol. Simul. 10,291−308 (1993)
[2] Post, Wolf, Stock, J. Chem. Phys 150, 101063 (2019)
[3] Wolf, Stock, J. Chem. Theory Comput. 14, 6175−6182 (2018)
[4] Falk, Savio, Moseler, Phys. Rev. Lett. 124, 105501 (2020)