Molecular Dynamics: Concept, Tools, Workflow and Applications
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2025
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| _version_ | 1866902206154801152 |
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| author | Vaishnavi Chavan, Amruta Kale, Prerana Panchwagh, Monika Shinde, Sagar Kale, Utkarsha Chavan |
| author_facet | Vaishnavi Chavan, Amruta Kale, Prerana Panchwagh, Monika Shinde, Sagar Kale, Utkarsha Chavan |
| contents | <p>A computer simulation of atoms and molecules moving physically is called molecular dynamics or MD. The numerical solution of the classical equation of motion step-by-step makes up molecular dynamics. The goal of molecular dynamics is to improve the current drug discovery process. We provide a general overview of the tools, force-field, stages, applications, limitations, and future prospects of molecular dynamics in this paper. Molecular dynamics is performed using tools such as GROMACS, AMBER, CHARMM-GUI, NAMD, and LAMMPS. The term force-field refers to the variety of interatomic potentials that we discuss here. More specifically, the functional form and parameter sets needed to determine a system's potential energy at the atomistic level are referred to as the force-field. In this review, we provide details on the steps that are crucial for doing molecular dynamics. MD can be used for docking, protein folding, membrane proteins, structure refinement, predicting molecular flexibility, examining how stimulation influences interaction, and biomedical applications.</p> |
| format | Recurso digital |
| id | zenodo_https___doi_org_10_5281_zenodo_15854972 |
| institution | Zenodo |
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| publishDate | 2025 |
| publisher | Zenodo |
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| spellingShingle | Molecular Dynamics: Concept, Tools, Workflow and Applications Vaishnavi Chavan, Amruta Kale, Prerana Panchwagh, Monika Shinde, Sagar Kale, Utkarsha Chavan Molecular dynamics, drug development, tools, steps. <p>A computer simulation of atoms and molecules moving physically is called molecular dynamics or MD. The numerical solution of the classical equation of motion step-by-step makes up molecular dynamics. The goal of molecular dynamics is to improve the current drug discovery process. We provide a general overview of the tools, force-field, stages, applications, limitations, and future prospects of molecular dynamics in this paper. Molecular dynamics is performed using tools such as GROMACS, AMBER, CHARMM-GUI, NAMD, and LAMMPS. The term force-field refers to the variety of interatomic potentials that we discuss here. More specifically, the functional form and parameter sets needed to determine a system's potential energy at the atomistic level are referred to as the force-field. In this review, we provide details on the steps that are crucial for doing molecular dynamics. MD can be used for docking, protein folding, membrane proteins, structure refinement, predicting molecular flexibility, examining how stimulation influences interaction, and biomedical applications.</p> |
| title | Molecular Dynamics: Concept, Tools, Workflow and Applications |
| topic | Molecular dynamics, drug development, tools, steps. |
| url | https://doi.org/10.5281/zenodo.15854972 |