Essential energy space random walks to accelerate molecular dynamics simulations: Convergence improvements via an adaptive-length self-healing strategy

2008 ◽  
Vol 129 (1) ◽  
pp. 014105 ◽  
Author(s):  
Lianqing Zheng ◽  
Wei Yang
Keyword(s):  
Molecular Dynamics ◽  
Random Walks ◽  
Molecular Dynamics Simulations ◽  
Energy Space ◽  
Self Healing ◽  
Dynamics Simulations

scholarly journals Molecular dynamics simulations on self-healing behavior of ionene polymer-based nanostructured hydrogels

Polymer ◽  
2020 ◽  
Vol 211 ◽  
pp. 123072
Author(s):  
Oscar Bertran ◽  
César Saldías ◽  
David Díaz Díaz ◽  
Carlos Alemán
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Self Healing ◽  
Dynamics Simulations ◽  
Ionene Polymer

Enhanced self-healing performance of graphene oxide/vitrimer nanocomposites: A molecular dynamics simulations study

Polymer ◽  
2020 ◽  
Vol 206 ◽  
pp. 122862
Author(s):  
Chanwook Park ◽  
Geonwoo Kim ◽  
Jiwon Jung ◽  
Balaji Krishnakumar ◽  
Sravendra Rana ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Graphene Oxide ◽  
Molecular Dynamics Simulations ◽  
Self Healing ◽  
Dynamics Simulations

Molecular dynamics simulations on self-healing behavior of photo-polymerization network

2018 ◽  
Vol 27 (10) ◽  
pp. 105013 ◽  
Author(s):  
Xiangrui Zheng ◽  
Hua Yang ◽  
Yaguang Sun ◽  
Yongqin Zhang ◽  
Yafang Guo
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Self Healing ◽  
Photo Polymerization ◽  
Dynamics Simulations

Molecular Dynamics Simulations of Self-Healing Topological Copolymers with a Comblike Structure

2021 ◽  
Vol 54 (3) ◽  
pp. 1095-1105
Author(s):  
Yue Fang ◽  
Tongkui Yue ◽  
Sai Li ◽  
Zhiyu Zhang ◽  
Jun Liu ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Self Healing ◽  
Dynamics Simulations

scholarly journals Effects of number of parallel runs and frequency of bias-strength replacement in generalized ensemble molecular dynamics simulations

2019 ◽  
Vol 1 ◽  
pp. e4 ◽  
Author(s):  
Takuya Shimato ◽  
Kota Kasahara ◽  
Junichi Higo ◽  
Takuya Takahashi
Keyword(s):  
Molecular Dynamics ◽  
Potential Energy ◽  
Molecular Dynamics Simulations ◽  
Conformational Changes ◽  
High Frequency ◽  
Md Simulations ◽  
Energy Space ◽  
Bias Potential ◽  
Ensemble Approach ◽  
Dynamics Simulations

Background The generalized ensemble approach with the molecular dynamics (MD) method has been widely utilized. This approach usually has two features. (i) A bias potential, whose strength is replaced during a simulation, is applied. (ii) Sampling can be performed by many parallel runs of simulations. Although the frequency of the bias-strength replacement and the number of parallel runs can be adjusted, the effects of these settings on the resultant ensemble remain unclear. Method In this study, we performed multicanonical MD simulations for a foldable mini-protein (Trp-cage) and two unstructured peptides (8- and 20-residue poly-glutamic acids) with various settings. Results As a result, running many short simulations yielded robust results for the Trp-cage model. Regarding the frequency of the bias-potential replacement, although using a high frequency enhanced the traversals in the potential energy space, it did not promote conformational changes in all the systems.

scholarly journals SELF-HEALING NANOMATERIALS: MULTIMILLION-ATOM REACTIVE MOLECULAR DYNAMICS SIMULATIONS

2017 ◽  
Author(s):  
Tomoya Hakamata ◽  
Kohei Shimamura ◽  
Fuyuki Shimojo ◽  
Rajiv K. Kalia ◽  
Aiichiro Nakano ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Self Healing ◽  
Reactive Molecular Dynamics ◽  
Dynamics Simulations
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