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. 2024 Jun 3;40(6):btae313.
doi: 10.1093/bioinformatics/btae313.

MolDy: molecular dynamics simulation made easy

Mohd Imran Khan  1 , Sheetal Pathania  1 , Mohammed W Al-Rabia  2   3 , Abdul S Ethayathulla  4 , Mohammad Imran Khan  5 , Khaled S Allemailem  6 , Mohd Azam  6 , Gururao Hariprasad  4 , Mohammad Azhar Imran  1
Affiliations

MolDy: molecular dynamics simulation made easy

Mohd Imran Khan et al. Bioinformatics. .

Abstract

Motivation: Molecular dynamics (MD) is a computational experiment that is crucial for understanding the structure of biological macro and micro molecules, their folding, and the inter-molecular interactions. Accurate knowledge of these structural features is the cornerstone in drug development and elucidating macromolecules functions. The open-source GROMACS biomolecular MD simulation program is recognized as a reliable and frequently used simulation program for its precision. However, the user requires expertise, and scripting skills to carrying out MD simulations.

Results: We have developed an end-to-end interactive MD simulation application, MolDy for Gromacs. This front-end application provides a customizable user interface integrated with the Python and Perl-based logical backend connecting the Linux shell and Gromacs software. The tool performs analysis and provides the user with simulation trajectories and graphical representations of relevant biophysical parameters. The advantages of MolDy are (i) user-friendly, does not requiring the researcher to have prior knowledge of Linux; (ii) easy installation by a single command; (iii) freely available for academic research; (iv) can run with minimum configuration of operating systems; (v) has valid default prefilled parameters for beginners, and at the same time provides scope for modifications for expert users.

Availability and implementation: MolDy is available freely as compressed source code files with user manual for installation and operation on GitHub: https://github.com/AIBResearchMolDy/Moldyv01.git and on https://aibresearch.com/innovations.

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Conflict of interest statement

None.

Figures

Figure 1.
Figure 1.
Installation, process flowchart depicting entire process of the application and snapshots of MolDy application windows. (A) A brief diagrammatic description of the MolDy architecture; (B) installation and process followed by MolDy to perform MD simulation; (C) diagrammatic representation of MolDy front end Initialization window; (D) open experiment window; (E) dynamics window of protein-based simulation experiments; (F) dynamics window of protein–ligand complex-based simulation experiments; (G) analysis window; (H) restart and extend window; (I) help window.
See this image and copyright information in PMC

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