×

Indexed by

Free-Energy Surface Prediction by Flying Gaussian Method

Vojtech Spiwok1*, Zoran Sucur1*

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

* Corresponding authors emails: spiwokv@vscht.cz, sucurz@vscht.cz
DOI10.24435/materialscloud:2019.0032/v1 [version v1]

Publication date: Jun 18, 2019

How to cite this record

Vojtech Spiwok, Zoran Sucur, Free-Energy Surface Prediction by Flying Gaussian Method, Materials Cloud Archive 2019.0032/v1 (2019), doi: 10.24435/materialscloud:2019.0032/v1.

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.

Materials Cloud sections using this data

No Explore or Discover sections associated with this archive record.

Files

File name Size Description
flyinggaussian.zip
MD5md5:a1116b8f5314984c4ec0b3fdd78b5ce7
25.2 MiB Input files (input structures, topology, Plumed input files) for simulations used to demonstrate functionality of Flying Gaussian algorithm (J. Chem. Theory Comput. 2016, 12, 4644-4650). The method simulates a molecular system in multiple replicas and enhances sampling by disfavoring states that are close to each other in different replicas. Input files for Flying Gaussian simulation of alanine dipeptide in vacuum and water, cis/trans isomerization of Ace-(Pro)n-NH2 and Met-enkephalin are provided.
README.txt
MD5md5:3016448d5245d46e047df8b26de5a167
2.5 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.
Metadata, except for email addresses, are licensed under the Creative Commons Attribution Share-Alike 4.0 International license.

External 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

Keywords

enhanced sampling molecular dynamics simulation free energy metadynamics

Version history:

2019.0032/v1 (version v1) [This version] Jun 18, 2019 DOI10.24435/materialscloud:2019.0032/v1