Free-Energy Surface Prediction by Flying Gaussian Method: Numerical Proof
- University of Chemistry and Technology, Prague
DOI10.24435/materialscloud:2019.0013/v1 (version v1, submitted on 17 April 2019)
How to cite this entry
Vojtech Spiwok, Zoran Šućur, Pavel Kříž, Free-Energy Surface Prediction by Flying Gaussian Method: Numerical Proof, Materials Cloud Archive (2019), doi: 10.24435/materialscloud:2019.0013/v1.
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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|1.1 MiB||Input files (input structure, topology, Plumed input) for a simple simulation used to demonstrate that free energy surface can be calculated from Flying Gaussians results using Umbrella Sampling reweighing, despite the dynamic nature of the bias potential. Tested on OpenMPI4.0.0, Gromacs 2018.5 and Plumed2.5.0. Script provided.|
|1.2 KiB||README.txt file with descriptions.
17 April 2019 [This version]