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Introduction of steered molecular dynamics into UNRES coarse-grained simulations package.

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Title: Introduction of steered molecular dynamics into UNRES coarse-grained simulations package.
Authors: Sieradzan, Adam K.1 adasko@sun1.chem.univ.gda.pl, Jakubowski, Rafał2
Source: Journal of Computational Chemistry. 3/30/2017, Vol. 38 Issue 8, p553-562. 10p.
Subjects: Molecular dynamics, Simulation methods & models, Atomic force microscopy, Molecular force constants, Ostwald ripening
Abstract: In this article, an implementation of steered molecular dynamics (SMD) in coarse-grain UNited RESidue (UNRES) simulations package is presented. Two variants of SMD have been implemented: with a constant force and a constant velocity. The huge advantage of SMD implementation in the UNRES force field is that it allows to pull with the speed significantly lower than the accessible pulling speed in simulations with all-atom representation of a system, with respect to a reasonable computational time. Therefore, obtaining pulling speed closer to those which appear in the atomic force spectroscopy is possible. The newly implemented method has been tested for behavior in a microcanonical run to verify the influence of introduction of artificial constrains on keeping total energy of the system. Moreover, as time dependent artificial force was introduced, the thermostat behavior was tested. The new method was also tested via unfolding of the Fn3 domain of human contactin 1 protein and the I27 titin domain. Obtained results were compared with Gø-like force field, all-atom force field, and experimental results. © 2017 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.)
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DbLabel: Engineering Source
An: 121000385
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PubType: Academic Journal
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  Data: Introduction of steered molecular dynamics into UNRES coarse-grained simulations package.
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  Data: <searchLink fieldCode="JN" term="%22Journal+of+Computational+Chemistry%22">Journal of Computational Chemistry</searchLink>. 3/30/2017, Vol. 38 Issue 8, p553-562. 10p.
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  Data: <searchLink fieldCode="DE" term="%22Molecular+dynamics%22">Molecular dynamics</searchLink><br /><searchLink fieldCode="DE" term="%22Simulation+methods+%26+models%22">Simulation methods & models</searchLink><br /><searchLink fieldCode="DE" term="%22Atomic+force+microscopy%22">Atomic force microscopy</searchLink><br /><searchLink fieldCode="DE" term="%22Molecular+force+constants%22">Molecular force constants</searchLink><br /><searchLink fieldCode="DE" term="%22Ostwald+ripening%22">Ostwald ripening</searchLink>
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  Data: In this article, an implementation of steered molecular dynamics (SMD) in coarse-grain UNited RESidue (UNRES) simulations package is presented. Two variants of SMD have been implemented: with a constant force and a constant velocity. The huge advantage of SMD implementation in the UNRES force field is that it allows to pull with the speed significantly lower than the accessible pulling speed in simulations with all-atom representation of a system, with respect to a reasonable computational time. Therefore, obtaining pulling speed closer to those which appear in the atomic force spectroscopy is possible. The newly implemented method has been tested for behavior in a microcanonical run to verify the influence of introduction of artificial constrains on keeping total energy of the system. Moreover, as time dependent artificial force was introduced, the thermostat behavior was tested. The new method was also tested via unfolding of the Fn3 domain of human contactin 1 protein and the I27 titin domain. Obtained results were compared with Gø-like force field, all-atom force field, and experimental results. © 2017 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.)
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        Value: 10.1002/jcc.24685
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      – Code: eng
        Text: English
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        PageCount: 10
        StartPage: 553
    Subjects:
      – SubjectFull: Molecular dynamics
        Type: general
      – SubjectFull: Simulation methods & models
        Type: general
      – SubjectFull: Atomic force microscopy
        Type: general
      – SubjectFull: Molecular force constants
        Type: general
      – SubjectFull: Ostwald ripening
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      – TitleFull: Introduction of steered molecular dynamics into UNRES coarse-grained simulations package.
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              M: 03
              Text: 3/30/2017
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              Y: 2017
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              Value: 38
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