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Protein–Ligand Complex MD Simulation

Step-by-step protein–ligand/drug molecular dynamics simulation using GROMACS, CHARMM36 force field, and key analyses including RMSD, RMSF, Rg, SASA, and binding free energy analysis.

Illustration of a protein–ligand molecular dynamics simulation workflow showing GROMACS setup, CHARMM36 force field, and analysis steps including RMSD, RMSF, Rg, SASA, and binding free energy
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Protein Molecular Dynamics Simulation

Step-by-step workflow for protein MD simulation using GROMACS, CHARMM36 force field, RMSD, RMSF, Rg, SASA and binding free energy analysis.

A 3D scientific visualization of a molecular dynamics (MD) simulation box. The transparent cube contains a multi-colored protein (teal, purple, gold), surrounded by water solvent (blue cloud and individual molecules), sodium ions (green spheres), and chloride ions (orange spheres). Text labels point to each component
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Virtual Screening, Drug build, Optimization & Non-covalent & Covalent Docking

 

Step-by-step virtual screening and drug design using molecular building, geometry optimization, docking, and key analyses, including binding affinity, interaction profiling & docking pose validation

Virtual Screening, Drug build, Optimization & Non-covalent & Covalent Docking
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SMD & Umbrella Sampling Simulation

Step-by-step SMD and umbrella sampling simulation using GROMACS, CHARMM36 force field, and key analyses including pulling force, WHAM, PMF, and binding free energy profile analysis.

SMD and umbrella sampling simulation workflow showing molecular pulling, sampling windows, and PMF-free energy analysis.
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Membrane (Lipid)-Protein Simulation

Step-by-step using GROMACS, CHARMM36 lipid force field, and key analyses including membrane thickness, area per lipid, lipid order parameters, density profile, and protein–lipid interaction analysis

Membrane (Lipid)-Protein Simulation
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Solvent Molecular Dynamics Simulation

Step-by-step solvent molecular dynamics simulation using GROMACS,  and key analyses including density, RDF, hydrogen bonding, MSD, diffusion coefficient, and solvent structure– profile analysis.

Solvent Molecular Dynamics Simulation
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