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Project B03: Coarse-graining of solvent effects in force-probe molecular dynamics simulations
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project-b03-coarse-graining-of-solvent-effects-in-force-probe-molecular-dynamics-simulations
Description:
The study of the conformational kinetics of biomolecules and supramolecular complexes using molecular simulations often is complicated by the fact that these processes are very slow. Various simulation techniques have been developed in order to resolve this issue. One very efficient way to investigate the atomistic details of conformational changes is provided by force-probe molecular dynamics (FPMD) simulations. In the most common realization of this technique, one end of the (supra)molecular system under consideration is fixed in space and the other end is pulled apart with a constant velocity via the application of a harmonic potential. From the distributions of the forces needed to unfold the system important information regarding the kinetics and the thermodynamics of the relevant conformational rearrangements can be obtained via a statistical analysis. The direct comparison to the results of experimental realizations of force spectroscopy usually is not easy due to the very different pulling velocities. Typically, these are about 5 orders of magnitude larger in FPMD simulations than in experiments. Therefore, every speed-up of FPMD simulations is highly desirable. A common procedure to speed up such calculations considerably is to use coarse-grained (CG) models. However, the details of the unfolding pathways cannot be monitored due to the loss of atomistic resolution.
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