materialscloud:2019.0013/v1

Free-Energy Surface Prediction by Flying Gaussian Method: Numerical Proof

Vojtech Spiwok1*, Zoran Šućur1*, Pavel Kříž1*

1 University of Chemistry and Technology, Prague

* Corresponding authors emails: spiwokv@vscht.cz , sucurz@vscht.cz , krizp@vscht.cz
DOI10.24435/materialscloud:2019.0013/v1 [version v1]

Publication date: Apr 17, 2019

How to cite this record

Vojtech Spiwok, Zoran Šućur, Pavel Kříž, Free-Energy Surface Prediction by Flying Gaussian Method: Numerical Proof, Materials Cloud Archive 2019.0013/v1 (2019), doi: 10.24435/materialscloud:2019.0013/v1.

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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Files

File name Size Description
flyinggaussian2.zip
MD5md5:4acf8cde64782dcea61e991f091129f7
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.
README.txt
MD5md5:f6727be8f7a558b4bb390642de346027
1.2 KiB README.txt file with descriptions.

License

Files and data are licensed under the terms of the following license: Creative Commons Attribution 4.0 International.

External 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

Keywords

metadynamics flying Gaussian method molecular dynamics simulation sampling

Version history:

2019.0013/v1 (version v1) [This version] Apr 17, 2019 DOI10.24435/materialscloud:2019.0013/v1