Jana Hozzova^1*, Ales Krenek^1*, Maria Simkova¹, Vojtech Spiwok^2*

1 Institute of Computer Science, Masaryk University, Brno, Czech Republic

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

* Corresponding authors emails: hozzova@ics.muni.cz, ljocha@ics.muni.cz, spiwokv@vscht.cz

DOI10.24435/materialscloud:2019.0021/v2 [version v2]

Publication date: Jun 17, 2019

How to cite this record

Jana Hozzova, Ales Krenek, Maria Simkova, Vojtech Spiwok, Reducing the Number of Mean-Square Deviation Calculations with Floating Close Structure in Metadynamics, Materials Cloud Archive 2019.0021/v2 (2019), https://doi.org/10.24435/materialscloud:2019.0021/v2

Description

Biomolecular simulations are computationally expensive. This limits their application in protein folding simulations, protein engineering, drug design and related fields. Enhanced sampling techniques such as metadynamics accelerates slow events in molecular simulation. This and other method apply artificial forces in directions of collective degrees of freedom (aka collective variables). Path collective variables and Property Map collective variables are defined using a series of reference structures of the studied molecular system. They require a huge number of mean square deviation calculations along the simulation. Close Structure algorithm reduces the number of these operations.

Materials Cloud sections using this data

Files

File name	Size	Description
README.txt MD5md5:674d0c753da4a27dd725796bcea1eff4	1.9 KiB	README.txt file with descriptions.
close_structure.zip MD5md5:159496266f331bdc777f4959ab2174eb	62.7 MiB	Input files (input structures, topology, Plumed input) for simulations used to demonstrate functionality of Close Structure algorithm (J. Chem. Phys. 2017, 146, 115101). The method replaces frequent calculations of root mean square deviations in Path collective variables or Property Map collective variables. This accelerates simulations. Input files for metadynamics simulation of cyclooctane derivative in vacuum and Trp-cage in implicit solvent with two or three, respectively, Isomap CVs (with and without Close Structure). Tested on OpenMPI4.0.0, Gromacs 2018.5 and Plumed2.5.0. Scripts provided.

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

Keywords

metadynamics collective variable mean square deviation