Published June 18, 2019 | Version v1
Dataset Open

Free-Energy Surface Prediction by Flying Gaussian Method

  • 1. Department of Biochemistry and Microbiology, University of Chemistry and Technology, Prague

* Contact person

Description

Molecular simulations are computationally expensive, especially in systems with multiple free energy minima. To address this problem many enhanced sampling techniques have been developed. Metadynamics uses a bias potential defined as a sum of Gaussian hills in space of few (one or two) collective variables. This bias potential disfavors states that have been visited since the beginning of the simulation. Multiple walker metadynamics simulates the system in multiple parallel replicas. The bias potential disfavors states that have been visited since the beginning of the simulation in any replica. Flying Gaussian method presented here also simulates the system in multiple parallel replicas. It disfavors states that are, at certain moment, similar in two or more replicas. It was demonstrated on Alanine Dipeptide in vacuum and water, cis/trans-isomerisation of Proline-containing peptides and Met-enkephalin.

Files

File preview

files_description.md

All files

Files (25.2 MiB)

Name Size
md5:1ad0416e232a2468047e97c0d939f048
701 Bytes Preview Download
md5:a1116b8f5314984c4ec0b3fdd78b5ce7
25.2 MiB Preview Download
md5:3016448d5245d46e047df8b26de5a167
2.5 KiB Preview Download

References

Journal reference (Paper introducing Flying Gaussian method)
Z. Sucur, V. Spiwok, J. Chem. Theory Comput. 12(9), 4644-4650 (2016), doi: 10.1021/acs.jctc.6b00551