Scymol: A python-based software package for initializing and running molecular dynamics simulations using LAMMPS

Eli I. Assaf*, Elsa Maalouf*, Xueyan Liu, Peng Lin, Sandra Erkens

*Corresponding author for this work

Research output: Contribution to journalArticleScientificpeer-review

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Abstract

Scymol is a Python-based software package specifically designed to facilitate the setup and execution of molecular simulations in LAMMPS. It comes equipped with a user-friendly interface, which simplifies the process of initializing molecular systems and defining simulation parameters. Moreover, the software generates and executes LAMMPS simulation sequences, enabling researchers to establish comprehensive simulation schemes, such as heating or deformation cycles, in a single run. Through its successful application in diverse research projects and its modular design, Scymol demonstrates considerable promise as an indispensable tool for researchers aiming to carry out molecular dynamics simulations without sacrificing complexity or high-throughput capabilities in their methodologies.
Original languageEnglish
Article number102044
Number of pages9
JournalSoftwareX
Volume29
DOIs
Publication statusPublished - 2025

Keywords

  • Computational Chemistry
  • Graphical User Interface
  • High Throughput
  • LAMMPS
  • Molecular Dynamics Simulations
  • Software Package

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