Algorithmic graph theory for post-processing molecular dynamics trajectories

被引：6

作者：

Bougueroua, Sana ^{[1
]}

Aboulfath, Ylene ^{[2
]}

Barth, Dominique ^{[2
]}

Gaigeot, Marie-Pierre ^{[1
]}

机构：

[1] Univ Paris Saclay, Univ Evry, CNRS, LAMBE UMR8587, Courcouronnes, France

[2] Univ Paris Saclay, Univ Versailles SQ, DAVID, Versailles, France

来源：

MOLECULAR PHYSICS | 2023年 / 121卷 / 7-8期

关键词：

Molecular dynamics; topological graph; graph of transition; graph of cycles; collective H-bonded network; AB-INITIO; SIMULATIONS; PREDICTION; INTERFACES; FIND; TOOL;

D O I：

10.1080/00268976.2022.2162456

中图分类号：

O64 [物理化学（理论化学）、化学物理学];

学科分类号：

070304 ; 081704 ;

摘要：

This paper reviews some of the graph theory-based methods that were recently developed in our group for post-processing molecular dynamics trajectories. We show that the use of algorithmic graph theory not only provides a direct and fast methodology to identify conformers that are sampled over time, but it also allows to follow in time the interconversions between the conformers through graphs of transitions, also provides statistical characterisations, that would otherwise be hard to obtain. Examples for a gas phase peptide and for the more complex inhomogeneous charged air-liquid water interface are presented in order to demonstrate the power of topological 2D-graphs and their versatility and transferability.

引用

页数：14

共 52 条

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