Molecular Dynamics

Full GROMACSMolecular Dynamics Pipeline.
Real-Time 3D Visualization.

Complete molecular dynamics simulation from topology generation to MM-PBSA binding energy calculation. Three force fields, automated trajectory analysis, and interactive 3D visualization with 3Dmol.jsinteractive 3D.

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10-STAGE PIPELINE

End-to-End MD Workflow

From raw PDB structure to binding energy calculation. Every stage is automated, validated, and reproducible.

Stage 01

Topology Generation

Convert PDB to GROMACSmolecular dynamics engine topology. Assign force field parameters, define atom types, and generate position restraints.

Stage 02

Solvation

Place protein in a cubic or dodecahedral box. Fill with TIP3P/SPC water model. Set minimum distance to box edge (1.0-1.2 nm).

Stage 03

Ion Addition

Neutralize system charge with Na+/Cl- counterions. Add physiological salt concentration (150 mM NaCl).

Stage 04

Energy Minimization

Steepest descent minimization to remove steric clashes. Converge to maximum force < 1000 kJ/mol/nm.

Stage 05

NVT Equilibration

100 ps constant volume/temperature equilibration. V-rescale thermostat at 300K. Position restraints on protein heavy atoms.

Stage 06

NPT Equilibration

100 ps constant pressure/temperature equilibration. Parrinello-Rahman barostat at 1 bar. Validate density convergence.

Stage 07

Production MD

10-100 ns production run. 2 fs timestep with LINCS constraints. PME electrostatics. Save coordinates every 10 ps.

Stage 08

Trajectory Analysis

RMSD, RMSF, radius of gyration, hydrogen bond analysis, secondary structure evolution (DSSP), PCA of conformational dynamics.

Stage 09

MM-PBSA Binding Energy

Calculate binding free energy decomposition: van der Waals, electrostatic, polar solvation, non-polar solvation, and entropy contributions.

Stage 10

3D Visualization

Interactive 3Dmol.jsinteractive 3D viewer with hydrogen bonds, binding hotspots, electrostatic surface, and trajectory animation. Exportable as images and movies.

FORCE FIELDS

Three Production Force Fields

Choose the force field best suited to your system. Each has been extensively validated for different biomolecular classes.

AMBER99SB-ILDNAll-Atom Protein FF

All-Atom Protein FF

Gold standard for protein simulations. Improved backbone torsion parameters (ILDN). Excellent for protein folding and conformational sampling.

CHARMM27Nucleic Acid FF

Nucleic Acid Compatible

Optimized for protein-nucleic acid systems. CMAP corrections for backbone. Compatible with CHARMM-GUI generated topologies for complex assemblies.

OPLS-AASmall Molecule FF

Small Molecule Optimized

Optimized for organic molecules and drug-like compounds. Excellent Lennard-Jones parameters for protein-ligand binding free energy calculations.

VISUALIZATION

Interactive 3D Analysis

Every MD simulation includes interactive 3Dmol.jsinteractive 3D visualizations showing hydrogen bonds, binding hotspots, and real-time trajectory playback.

3dmol_viewer.html — MD Trajectory Analysis

H-Bonds

14 stable

RMSD

1.8 +/- 0.3 A

Binding dG

-42.3 kJ/mol

Trajectory

50 ns / 5000 frames

BINDING ENERGY

MM-PBSA Free Energy Decomposition

Quantitative binding energy calculation with per-residue decomposition. Identify the key interactions driving ligand binding.

Energy Components

The MM-PBSA method decomposes the binding free energy into physically meaningful components, revealing whether binding is driven by electrostatics, van der Waals contacts, or desolvation.

dG_bind = dE_MM + dG_solv - TdS

vdW

Van der Waals

Lennard-Jones interactions between protein and ligand

Elec

Electrostatic

Coulomb interactions from charged/polar groups

Polar Solvation

Poisson-Boltzmann implicit solvent contribution

Non-Polar Solvation

Solvent-accessible surface area hydrophobic term

-TS

Entropy

Conformational entropy penalty from binding

Full GROMACSMolecular Dynamics Pipeline.Real-Time 3D Visualization.