Seonghyun Park

AMD is a localhost web application for running GROMACS + PLUMED molecular dynamics simulations through a browser GUI. Configure parameters, visualize molecules, launch simulations, and analyze results — all without touching the command line. Runs locally on your machine via Docker.

1. Log In

Open http://localhost:8000 and sign in. Each user gets their own sessions and settings stored in a local SQLite database.

2. Create a New Session

The main dashboard shows a sidebar for managing sessions. Click + New Session to start.

The session creation screen lets you configure three things:

• Molecule System — Alanine Dipeptide, Chignolin (CLN025), Trp-cage, BBA, or Blank for custom uploads
• Simulation Method — Molecular Dynamics, Metadynamics, OPES, Umbrella Sampling, or Steered MD
• GROMACS Template — Default, Quick, Long, or Total presets that auto-fill parameters

For this tutorial, select Chignolin (CLN025), Metadynamics, and the Default template.

3. Load and Inspect the Molecule

The Molecule tab renders chignolin in an interactive NGL 3D viewer with Ball+Stick, Cartoon, and Surface representations.

Below, the Molecule Files panel lists all PDB files — original structure, processed conformations, and topology files. Upload additional files by dragging them in, or search RCSB directly.

4. Configure GROMACS Parameters

The GROMACS tab provides full control over simulation parameters:

• System — force field (CHARMM27), solvent (Vacuum), box type (Cubic), box clearance, compute device (GPU/CPU)
• Simulation Length — number of steps (500,000) and timestep (2 fs)
• Temperature — reference temperature (300 K) and thermostat time constant (0.1 ps)
• Advanced Parameters — Coulomb/VdW cutoffs, electrostatics type (PME), PME order, Fourier spacing

Suggest Settings (TBA) — AI-powered parameter recommendations based on your molecule system and simulation method.

5. Set Up Metadynamics

The Method tab configures PLUMED enhanced sampling. Tabs at the top switch between MD, MetaD, OPES, Umbrella, and Steered.

For well-tempered metadynamics, set:

• Stride and Cutoff for hill deposition
• Height and Pace of the Gaussian hills
• Sigma and Bias factor for well-tempered behavior
• Temperature — must match the GROMACS thermostat

The Collective Variables section lets you define CVs interactively — click atoms on the 3D structure, or choose from presets: All CA distances, Consecutive CA distances, Backbone torsion angles (phi/psi), or custom selections.

Suggest CVs (TBA) — AI-assisted collective variable recommendations based on the molecule and sampling method.

Preview PLUMED — Preview of the PLUMED input file before launching.

6. Launch the Simulation

Click Start MD Simulation to see a summary dialog before running. It shows:

• Total simulation time and step count
• Output logging — each output file with its write frequency, number of frames, and estimated file size (e.g., xtc compressed trajectory at 10-step intervals, edr energy file, log file, HILLS and COLVAR from PLUMED)

Review the estimates, then click Run to launch. You can also go back to Edit Settings if anything needs adjustment.

7. Track Progress

While running, the Progress tab updates in real time:

• Run Summary — wall time, ETA, and performance (ns/day)
• Progress bar — current step out of total with completion percentage
• Trajectory — live 3D viewer showing chignolin after simulation has finished, with play/pause, reset, screenshot, and fullscreen controls

8. Analyze Results

Once the simulation finishes (green Simulation Finished banner), click + Add in the Results panel to select analyses such as potential energy, pressure, and Ramachandran plots.

Select the plots you want and click Run Analysis to generate them.

The Results panel then displays all analysis plots side by side — CV scatter plots, RMSD over time, pressure fluctuations, total energy, and more. Each plot is interactive and can be resized or rearranged.

AI Analysis (TBA) — automated interpretation of simulation results, identifying metastable states and convergence.

Tech Stack: TypeScript · Python · Jupyter Notebook · Shell

License: MIT