View in EDS

Introduction of periodic boundary conditions into UNRES force field.

Saved in:
Bibliographic Details
Title: Introduction of periodic boundary conditions into UNRES force field.
Authors: Sieradzan, Adam K.1
Source: Journal of Computational Chemistry. May2015, Vol. 36 Issue 12, p940-946. 7p.
Subjects: Boundary value problems, Molecular force constants, Simulation methods & models, Comparative studies, Electrostatic interaction
Abstract: In this article, implementation of periodic boundary conditions (PBC) into physics-based coarse-grained UNited RESidue (UNRES) force field is presented, which replaces droplet-like restraints previously used. Droplet-like restraints are necessary to keep multichain systems together and prevent them from dissolving to infinitely low concentration. As an alternative for droplet-like restrains cuboid PBCs with imaging of the molecules were introduced. Owing to this modification, artificial forces which arose from restraints keeping a droplet together were eliminated what leads to more realistic trajectories. Due to computational reasons cutoff and smoothing functions were introduced on the long range interactions. The UNRES force field with PBC was tested by performing microcanonical simulations. Moreover, to asses the behavior of the thermostat in PBCs Langevin and Berendsen thermostats were studied. The influence of PBCs on association pattern was compared with droplet-like restraints on the ββα hetero tetramer 1 protein system. © 2015 Wiley Periodicals, Inc. [ABSTRACT FROM AUTHOR]
Copyright of Journal of Computational Chemistry is the property of Wiley-Blackwell and its content may not be copied or emailed to multiple sites without the copyright holder's express written permission. Additionally, content may not be used with any artificial intelligence tools or machine learning technologies. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)
Database: Engineering Source
FullText Text:
  Availability: 0
Header DbId: egs
DbLabel: Engineering Source
An: 101965530
AccessLevel: 6
PubType: Academic Journal
PubTypeId: academicJournal
PreciseRelevancyScore: 0
IllustrationInfo
Items – Name: Title
  Label: Title
  Group: Ti
  Data: Introduction of periodic boundary conditions into UNRES force field.
– Name: Author
  Label: Authors
  Group: Au
  Data: <searchLink fieldCode="AR" term="%22Sieradzan%2C+Adam+K%2E%22">Sieradzan, Adam K.</searchLink><relatesTo>1</relatesTo>
– Name: TitleSource
  Label: Source
  Group: Src
  Data: <searchLink fieldCode="JN" term="%22Journal+of+Computational+Chemistry%22">Journal of Computational Chemistry</searchLink>. May2015, Vol. 36 Issue 12, p940-946. 7p.
– Name: Subject
  Label: Subjects
  Group: Su
  Data: <searchLink fieldCode="DE" term="%22Boundary+value+problems%22">Boundary value problems</searchLink><br /><searchLink fieldCode="DE" term="%22Molecular+force+constants%22">Molecular force constants</searchLink><br /><searchLink fieldCode="DE" term="%22Simulation+methods+%26+models%22">Simulation methods & models</searchLink><br /><searchLink fieldCode="DE" term="%22Comparative+studies%22">Comparative studies</searchLink><br /><searchLink fieldCode="DE" term="%22Electrostatic+interaction%22">Electrostatic interaction</searchLink>
– Name: Abstract
  Label: Abstract
  Group: Ab
  Data: In this article, implementation of periodic boundary conditions (PBC) into physics-based coarse-grained UNited RESidue (UNRES) force field is presented, which replaces droplet-like restraints previously used. Droplet-like restraints are necessary to keep multichain systems together and prevent them from dissolving to infinitely low concentration. As an alternative for droplet-like restrains cuboid PBCs with imaging of the molecules were introduced. Owing to this modification, artificial forces which arose from restraints keeping a droplet together were eliminated what leads to more realistic trajectories. Due to computational reasons cutoff and smoothing functions were introduced on the long range interactions. The UNRES force field with PBC was tested by performing microcanonical simulations. Moreover, to asses the behavior of the thermostat in PBCs Langevin and Berendsen thermostats were studied. The influence of PBCs on association pattern was compared with droplet-like restraints on the ββα hetero tetramer 1 protein system. © 2015 Wiley Periodicals, Inc. [ABSTRACT FROM AUTHOR]
– Name: AbstractSuppliedCopyright
  Label:
  Group: Ab
  Data: <i>Copyright of Journal of Computational Chemistry is the property of Wiley-Blackwell and its content may not be copied or emailed to multiple sites without the copyright holder's express written permission. Additionally, content may not be used with any artificial intelligence tools or machine learning technologies. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract.</i> (Copyright applies to all Abstracts.)
PLink https://search.ebscohost.com/login.aspx?direct=true&site=eds-live&db=egs&AN=101965530
RecordInfo BibRecord:
  BibEntity:
    Identifiers:
      – Type: doi
        Value: 10.1002/jcc.23864
    Languages:
      – Code: eng
        Text: English
    PhysicalDescription:
      Pagination:
        PageCount: 7
        StartPage: 940
    Subjects:
      – SubjectFull: Boundary value problems
        Type: general
      – SubjectFull: Molecular force constants
        Type: general
      – SubjectFull: Simulation methods & models
        Type: general
      – SubjectFull: Comparative studies
        Type: general
      – SubjectFull: Electrostatic interaction
        Type: general
    Titles:
      – TitleFull: Introduction of periodic boundary conditions into UNRES force field.
        Type: main
  BibRelationships:
    HasContributorRelationships:
      – PersonEntity:
          Name:
            NameFull: Sieradzan, Adam K.
    IsPartOfRelationships:
      – BibEntity:
          Dates:
            – D: 05
              M: 05
              Text: May2015
              Type: published
              Y: 2015
          Identifiers:
            – Type: issn-print
              Value: 01928651
          Numbering:
            – Type: volume
              Value: 36
            – Type: issue
              Value: 12
          Titles:
            – TitleFull: Journal of Computational Chemistry
              Type: main
ResultId 1