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d-SEAMS: Deferred Structural Elucidation Analysis for Molecular Simulations.

Rohit Goswami1, Amrita Goswami1, Jayant K Singh1

  • 1Department of Chemical Engineering, Indian Institute of Technology Kanpur, Kanpur 208016, Uttar Pradesh, India.

Journal of Chemical Information and Modeling
|March 21, 2020
PubMed
Summary
This summary is machine-generated.

d-SEAMS is a new open-source software tool for analyzing molecular dynamics simulations of water. It accurately classifies ice structures in confined and bulk systems, advancing nucleation research.

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Area of Science:

  • Computational physics and chemistry
  • Materials science
  • Chemical engineering

Background:

  • Accurate structural analysis is crucial for computational studies of water nucleation and supercooled states.
  • Understanding molecular mechanisms requires analyzing evolving ice-like structures, which is computationally intensive.

Purpose of the Study:

  • To introduce d-SEAMS, a free, open-source postprocessing engine for analyzing molecular dynamics trajectories.
  • To enable qualitative classification of ice structures in confined and bulk systems.
  • To provide user-friendly and extensible tools for advanced ice structure analysis.

Main Methods:

  • Implementation of recent algorithms for confined ice structure determination.
  • Application of topological network criteria for bulk ice structure analysis.
  • Proposal and validation of a novel order parameter for quasi-one-dimensional ice building blocks.
  • Development of a customizable code architecture using nix and a YAML-Lua scripting pipeline.

Main Results:

  • d-SEAMS successfully classifies ice structures in various systems, including confined and bulk water.
  • The software integrates novel algorithms and a new order parameter for enhanced structural identification.
  • Demonstrated analysis of heterogeneous ice nucleation on a β-AgI surface, homogeneous nucleation, and ice nanotube freezing.

Conclusions:

  • d-SEAMS offers a powerful, flexible, and user-friendly solution for analyzing complex ice nucleation and structure formation in molecular dynamics simulations.
  • The tool facilitates immediate visual insights and quantitative metrics, aiding researchers in understanding water's phase transitions.
  • d-SEAMS advances the field by providing accessible and state-of-the-art methods for ice structure determination.