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

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{
  "revision": 2, 
  "id": "133", 
  "created": "2020-05-12T13:52:48.379211+00:00", 
  "metadata": {
    "doi": "10.24435/materialscloud:2019.0021/v2", 
    "status": "published", 
    "title": "Reducing the Number of Mean-Square Deviation Calculations with Floating Close Structure in Metadynamics", 
    "mcid": "2019.0021/v2", 
    "license_addendum": "", 
    "_files": [
      {
        "description": "README.txt file with descriptions.", 
        "key": "README.txt", 
        "size": 1956, 
        "checksum": "md5:674d0c753da4a27dd725796bcea1eff4"
      }, 
      {
        "description": "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.", 
        "key": "close_structure.zip", 
        "size": 65709531, 
        "checksum": "md5:159496266f331bdc777f4959ab2174eb"
      }
    ], 
    "owner": 299, 
    "_oai": {
      "id": "oai:materialscloud.org:133"
    }, 
    "keywords": [
      "metadynamics", 
      "collective variable", 
      "mean square deviation"
    ], 
    "conceptrecid": "131", 
    "is_last": true, 
    "references": [
      {
        "type": "Journal reference", 
        "doi": "10.1063/1.4978296", 
        "url": "", 
        "comment": "Paper in which the Close Structure method for fast calculation of RMSD in Path and Property Map CVs is described", 
        "citation": "J. Hozzova (nee Pazurikova), A. Krenek, V. Spiwok, M. Simkova, J. Chem. Phys. 146, 115101 (2017)"
      }, 
      {
        "type": "Preprint", 
        "doi": "", 
        "url": "https://arxiv.org/abs/1801.02362v1", 
        "comment": "Paper in which the Close Structure method for fast calculation of RMSD in Path and Property Map CVs is thoroughly tested", 
        "citation": "J. Hozzova (nee Pazurikova), J. Olha, A. Krenek, V. Spiwok, arXiv:1801.02362"
      }
    ], 
    "publication_date": "Jun 17, 2019, 00:00:00", 
    "license": "Creative Commons Attribution 4.0 International", 
    "id": "133", 
    "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.", 
    "version": 2, 
    "contributors": [
      {
        "email": "hozzova@ics.muni.cz", 
        "affiliations": [
          "Institute of Computer Science, Masaryk University, Brno, Czech Republic"
        ], 
        "familyname": "Hozzova", 
        "givennames": "Jana"
      }, 
      {
        "email": "ljocha@ics.muni.cz", 
        "affiliations": [
          "Institute of Computer Science, Masaryk University, Brno, Czech Republic"
        ], 
        "familyname": "Krenek", 
        "givennames": "Ales"
      }, 
      {
        "affiliations": [
          "Institute of Computer Science, Masaryk University, Brno, Czech Republic"
        ], 
        "familyname": "Simkova", 
        "givennames": "Maria"
      }, 
      {
        "email": "spiwokv@vscht.cz", 
        "affiliations": [
          "Department of Biochemistry and Microbiology, University of Chemistry and Technology, Prague"
        ], 
        "familyname": "Spiwok", 
        "givennames": "Vojtech"
      }
    ], 
    "edited_by": 100
  }, 
  "updated": "2021-01-26T14:41:38.009217+00:00"
}