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| Format: | Recurso digital |
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2025
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| Online Access: | https://doi.org/10.5281/zenodo.17867493 |
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| _version_ | 1866902220799213568 |
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| author | Carvalho, Filipe André da Silva Maximiano, Pedro Simões, Pedro Nuno NL Hashemi, Mohtadin |
| author_facet | Carvalho, Filipe André da Silva Maximiano, Pedro Simões, Pedro Nuno NL Hashemi, Mohtadin |
| contents | <p>This dataset contains 500 ns all-atom Molecular Dynamics (MD) trajectories and analysis scripts for POPC bilayers, covering system sizes of 256, 512, and 1024 lipids at hydration levels of 40, 80, and 160 waters per lipid.</p> <p>The data supports a two-fold study:</p> <ol> <li> <p><strong>Biophysical Convergence:</strong> Assessing how structural properties (APL, thickness) and dynamic properties (order parameters, headgroup tilt, diffusion) converge as a function of membrane size and hydration.</p> </li> <li> <p><strong>Software Benchmarking:</strong> Comparing the accuracy and computational performance of four major analysis packages: <strong>CPPTRAJ</strong>, <strong>GROMACS</strong>, <strong>MDAnalysis</strong>, and <strong>LiPyphilic</strong>.</p> </li> </ol> <p><strong>Repository Contents</strong></p> <ul> <li> <p><strong>To reproduce the trajectory analysis </strong></p> <ul> <li> <p> Raw (continuous/unwrapped) and pre-processed (centered/imaged) trajectory files sampled at 1 ns/frame, topologies and index files (folder <a href="https://zenodo.org/api/records/17867493/draft/files/trajectories_topology_indices.zip/content" target="_blank" rel="noopener noreferrer">trajectories_topology_indices.zip</a>).</p> </li> <li>A complete set of Bash and Python scripts used to calculate Area Per Lipid (APL), Bilayer Thickness, SCD Order Parameters, Headgroup Orientation, and Lateral Diffusion (MSD), and software benchmark (folder <a href="https://zenodo.org/api/records/17867493/draft/files/scripts.zip/content" target="_blank" rel="noopener noreferrer">scripts</a>). </li> <li>Refer to the readme.md file for guidance. <br><br></li> </ul> </li> <li> <p><strong>To reproduce the Simulations </strong></p> <ul> <li> <p>Simulation topologies and index files required to reproduce the simulations (folder <a href="/records/17867493/files/MD_simulations_input&topology_files.zip?download=1">MD_simulations_input&topology_files.zip</a>).</p> </li> <li> <p>Refer to the readme.md for for guidance.</p> </li> </ul> </li> </ul> |
| format | Recurso digital |
| id | zenodo_https___doi_org_10_5281_zenodo_17867493 |
| institution | Zenodo |
| language | |
| publishDate | 2025 |
| publisher | Zenodo |
| record_format | zenodo |
| spellingShingle | Molecular Dynamics Simulation Dataset: POPC Bilayers at Varying Sizes (256, 512 and 1024 lipids) and Hydrations (40, 80 and 160 water/lipid) Analyzed with CPPTRAJ, GROMACS, MDAnalysis, and LiPyphilic Carvalho, Filipe André da Silva Maximiano, Pedro Simões, Pedro Nuno NL Hashemi, Mohtadin <p>This dataset contains 500 ns all-atom Molecular Dynamics (MD) trajectories and analysis scripts for POPC bilayers, covering system sizes of 256, 512, and 1024 lipids at hydration levels of 40, 80, and 160 waters per lipid.</p> <p>The data supports a two-fold study:</p> <ol> <li> <p><strong>Biophysical Convergence:</strong> Assessing how structural properties (APL, thickness) and dynamic properties (order parameters, headgroup tilt, diffusion) converge as a function of membrane size and hydration.</p> </li> <li> <p><strong>Software Benchmarking:</strong> Comparing the accuracy and computational performance of four major analysis packages: <strong>CPPTRAJ</strong>, <strong>GROMACS</strong>, <strong>MDAnalysis</strong>, and <strong>LiPyphilic</strong>.</p> </li> </ol> <p><strong>Repository Contents</strong></p> <ul> <li> <p><strong>To reproduce the trajectory analysis </strong></p> <ul> <li> <p> Raw (continuous/unwrapped) and pre-processed (centered/imaged) trajectory files sampled at 1 ns/frame, topologies and index files (folder <a href="https://zenodo.org/api/records/17867493/draft/files/trajectories_topology_indices.zip/content" target="_blank" rel="noopener noreferrer">trajectories_topology_indices.zip</a>).</p> </li> <li>A complete set of Bash and Python scripts used to calculate Area Per Lipid (APL), Bilayer Thickness, SCD Order Parameters, Headgroup Orientation, and Lateral Diffusion (MSD), and software benchmark (folder <a href="https://zenodo.org/api/records/17867493/draft/files/scripts.zip/content" target="_blank" rel="noopener noreferrer">scripts</a>). </li> <li>Refer to the readme.md file for guidance. <br><br></li> </ul> </li> <li> <p><strong>To reproduce the Simulations </strong></p> <ul> <li> <p>Simulation topologies and index files required to reproduce the simulations (folder <a href="/records/17867493/files/MD_simulations_input&topology_files.zip?download=1">MD_simulations_input&topology_files.zip</a>).</p> </li> <li> <p>Refer to the readme.md for for guidance.</p> </li> </ul> </li> </ul> |
| title | Molecular Dynamics Simulation Dataset: POPC Bilayers at Varying Sizes (256, 512 and 1024 lipids) and Hydrations (40, 80 and 160 water/lipid) Analyzed with CPPTRAJ, GROMACS, MDAnalysis, and LiPyphilic |
| url | https://doi.org/10.5281/zenodo.17867493 |