Published April 17, 2019 | Version v1
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Free-Energy Surface Prediction by Flying Gaussian Method: Numerical Proof

  • 1. University of Chemistry and Technology, Prague

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Description

Biomolecular simulations have a great potential in protein engineering, drug discovery and many other fields. Unfortunately, this method is computationally expensive, so many interesting processes cannot be routinely studied. In order to address this problem we developed Flying Gaussian method [Journal of Chemical Theory and Computation 12, 4644-4650 (2016)]. This method simultaneously simulates multiple replicas of the studied system and disfavor replicas with similar structures by artificial bias potential. The question arises how to calculate an unbiased free energy surface from a biased simulation. This dataset demonstrates together with mathematical arguments supports application of Umbrella Sampling reweighing method, despite the fact that this method is designed for methods with a time-independent bias potential.

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References

Journal reference (Paper in which we show that free energy surface from flying Gaussian method (Journal of Chemical Theory and Computation 12, 4644-4650 (2016)) can be calculated by umbrella sampling reweighing.)
P. Kříž, Z. Šućur, V. Spiwok, Journal of Physical Chemistry B 121, 10479-10483 (2017), doi: 10.1021/acs.jpcb.7b09337