Reducing the Number of Mean-Square Deviation Calculations with Floating Close Structure in Metadynamics

Authors: Jana Hozzova1*, Ales Krenek1*, Maria Simkova1, Vojtech Spiwok2*

  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, submitted on 17 June 2019)

How to cite this entry

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), doi: 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

No Explore or Discover sections associated with this archive entry.

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.

External references

Journal reference (Paper in which the Close Structure method for fast calculation of RMSD in Path and Property Map CVs is described)
J. Hozzova (nee Pazurikova), A. Krenek, V. Spiwok, M. Simkova, J. Chem. Phys. 146, 115101 (2017) doi:10.1063/1.4978296
Preprint (Paper in which the Close Structure method for fast calculation of RMSD in Path and Property Map CVs is thoroughly tested)

Keywords

metadynamics collective variable mean square deviation

Version history

17 June 2019 [This version]

17 May 2019