MOUSE2: Molecular Ordering Utilities for Simulations, Edition 2

Mikhail K. Glagolev; Anna A. Glagoleva; Valentina Vasilevskaya

doi:10.14529/jsfi230307

Authors

Mikhail K. Glagolev A. N. Nesmeyanov Institute for Organoelement Compounds RAS, Moscow, Russian Federation https://orcid.org/0000-0003-1128-649X
Anna A. Glagoleva A. N. Nesmeyanov Institute for Organoelement Compounds RAS, Moscow, Russian Federation https://orcid.org/0000-0002-6253-2382
Valentina Vasilevskaya A. N. Nesmeyanov Institute for Organoelement Compounds RAS, Moscow, Russian Federation; Chemistry Department, M. V. Lomonosov Moscow State University, Moscow, Russian Federation https://orcid.org/0000-0003-0623-0467

DOI:

https://doi.org/10.14529/jsfi230307

Keywords:

molecular simulation, polymers, helicity, simulation data processing, order parameters, performance optimization

Abstract

The progress in spatial and temporal scales of molecular simulations attainable with modern supercomputers makes the processing of the simulation data a challenging task in itself. One of the most important applications is simulation of living systems, which are based on polymers, as well as simulation of polymer systems in material sciences. The behavior of many polymer systems is determined by the local ordering of polymer chains, which on many occasions contain helical motifs. This ordering can be hard to quantify visually and using standard tools. To overcome these problems, we have developed an original toolkit to look into orientational and especially chiral ordering in polymer systems, which can quantify the orientational ordering of polymers based on their spatial proximity as well as assess the stiffness, helical and superhelical ordering based on polymer connectivity. The proposed software is aimed at balancing the flexibility and computational efficiency. The quantitative order parameters can be useful to quantify various types of self-organization observed in coarse-grained as well as all-atom particle simulations. The utilities can be tailored to meet specific user requirements.

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