Temperature dependent mechanical unfolding of calixarene nanocapsules studied by molecular dynamics simulations

Kato, Takashi; Schafer, K. J.; Jaschonek, Stefan; Gauß, Jürgen; Diezemann, Gregor

doi:10.1063/1.5111717

Cited by 2 publications

(1 citation statement)

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“…This finding is similar to what we have observed in temperature dependent AA simulations for increasing temperature [48]. We mention that the number of simulations performed (300 for each set of parameters) is not large enough for a detailed discussion of the shape and the widths of the distributions.…”

Section: Rupture Force Distributionssupporting

confidence: 89%

Force probe simulations using an adaptive resolution scheme

Oestereich,

Gauss,

Diezemann

2021

Preprint

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Molecular simulations of the forced unfolding and refolding of biomolecules or molecular complexes allow to gain important kinetic, structural and thermodynamic information about the folding process and the underlying energy landscape. In force probe molecular dynamics (FPMD) simulations, one pulls one end of the molecule with a constant velocity in order to induce the relevant conformational transitions. Since the extended configuration of the system has to fit into the simulation box together with the solvent such simulations are very time consuming. Here, we apply a hybrid scheme in which the solute is treated with atomistic resolution and the solvent molecules far away from the solute are described in a coarse-grained manner. We use the adaptive resolution scheme (AdResS) that has very successfully been applied to various examples of equilibrium simulations. We perform FPMD simulations using AdResS on a well studied system, a dimer formed from mechanically interlocked calixarene capsules. The results of the multiscale simulations are compared to all-atom simulations of the identical system and we observe that the size of the region in which atomistic resolution is required depends on the pulling velocity, i.e. the particular non-equilibrium situation. For large pulling velocities a larger all atom region is required. Our results show that multiscale simulations can be applied also in the strong non-equilibrium situations that the system experiences in FPMD simulations.

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Section: Rupture Force Distributionssupporting

confidence: 89%