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I will create professional protein ligand molecular dynamics notebook
Biotechnologist
Biotechnology undergraduate with a strong foundation in molecular biology, genetics, microbiology, and bioinformatics. Skilled in scientific writing, data analysis, and presenting complex concepts cle...
About this Gig
Looking for a scientifically rigorous molecular dynamics (MD) notebook to accelerate your research? I provide ready-to-use protein-ligand MD notebooks built with industry-standard methods, covering the entire pipeline from raw files to publication-ready analysis.
Whats Included:
- Solvated System: Explicit TIP3P water with 0.15 M NaCl.
- Equilibration: Energy minimization, NVT, and NPT protocols for a stable start.
- Production Trajectory: DCD format compatible with VMD, OVITO, and PyMOL.
- Comprehensive Analysis: A six-panel figure (RMSD, RMSF, Rg, etc.) and full energy logs.
- Reproducibility: All parameters saved in a configuration file with final PDB structures.
Scientific Standards:
- Force Fields: AMBER ff14SB (Protein) & OpenFF Sage (Ligand).
- Charges: AM1-BCC quantum mechanical method.
- Dynamics: Particle Mesh Ewald (PME) and Langevin Middle integrator (2 fs timestep).
Every notebook is citable and includes full literature references. Message me with your Protein PDB ID and Ligand SMILES/SDF before ordering to confirm compatibility and delivery timelines. Streamline your workflow with a professional tool designed for peer-reviewed excellence.
