VMDWeb

VMDWeb brings VMD-style molecular-dynamics visualization and trajectory analysis into ChemistryAtlas. The app uses NGL for an immediate browser preview, then sends topology, structure, trajectory, and atom-selection settings to backend VMD for scripted analysis.

Best For

• Molecular-dynamics trajectories and atom-selection analysis.
• RMSD, RMSF, contacts, hydrogen bonds, distance time series, frame extraction, and PBC cleanup.
• Uploading topology/structure plus trajectory files and generating reproducible VMD Tcl scripts.
• Browser trajectory animation and downloadable movie/GIF output for small or prepared trajectories.
• Checking that VMD is installed correctly on a local or remote ChemistryAtlas backend.

Inputs

• Structure/topology files: .pdb, .psf, .gro, .mol2, .cif, .xyz, and related VMD-readable files.
• Trajectory files: .dcd, .xtc, .trr, .nc, .lammpstrj, and related VMD-readable trajectory formats.
• VMD atom selections such as all, protein, protein and name CA, resname LIG, or within 4 of resname LIG.
• Workflow settings such as reference frame, stride, contact cutoff, hydrogen-bond cutoff, and command-runner Tcl.

Sample Files

VMDWeb includes a tiny demo system under /samples:

• vmdweb_demo_structure.pdb
• vmdweb_demo_topology.psf
• vmdweb_demo_trajectory.lammpstrj
• vmdweb_demo_bundle.zip

Upload the PDB, PSF, and LAMMPS trajectory together, choose RMSD vs frame, and use:

workflow=rmsd
selection=all
reference_frame=0
stride=1

The demo has only six atoms and five frames. It is meant for testing upload, preview, VMD execution, animation, and file export rather than scientific interpretation.

Multi-File Upload And Preview

Place the structure/topology and trajectory upload controls above the preview window. The NGL preview loads the currently selected structure/topology so you can check that the molecular system is recognizable before running VMD.

• Upload topology, structure, and trajectory files together when possible.
• Use the preview to inspect the structure file; VMD performs the trajectory analysis.
• Use Render to reload the active preview structure.
• Use Reset to restore the default preview orientation and zoom.

Workflows

RMSD vs Frame

Calculates RMSD for a VMD atom selection against a reference frame.

selection=protein and name CA
reference_frame=0
stride=1

RMSF

Calculates per-atom fluctuation values for a selection across the trajectory. Residue-level or backbone selections usually produce clearer reports.

Contacts

Counts contacts between two selections at each frame.

selection_a=protein
selection_b=not protein and not water
cutoff=4.0

Hydrogen Bonds

Counts hydrogen bonds between two selections over time. Defaults are typically 3.5 Angstrom and 30 degrees unless changed.

Distance Time Series

Measures the distance between the mass-weighted centers of two selections over each frame.

PBC Cleanup

Uses VMD/pbctools to wrap and center trajectories, then exports a cleaned DCD when periodic-cell information is available.

Frame Extraction

Exports a selected frame as PDB for downstream inspection, ChimeraX/PyMOL figure rendering, or notebook archiving.

Animate Trajectory In Browser

Loads a prepared trajectory preview into the browser when the trajectory format and size are suitable. For large trajectories, strip solvent, stride frames, or use a smaller representative segment before uploading.

Export Movie/GIF

Runs the configured VMD workflow and writes an animated output such as vmdweb-trajectory.gif when the backend has the required rendering utilities. The generated GIF appears in the job output/download list.

Command Runner

Runs advanced VMD Tcl supplied by the user. Use this only for reproducible internal scripts and avoid assumptions about paths outside the job working directory.

Backend Requirement

VMDWeb requires VMD on the backend. Set one of:

CHEMISTRYATLAS_VMD_BIN=/path/to/vmd
VMD_BIN=/path/to/vmd

or make vmd available on PATH. ChemistryAtlas runs:

vmd -dispdev text -e vmdweb-script.tcl

If VMD is missing, the backend job fails clearly while the browser preview remains available.

Troubleshooting

• VMD warnings about residue-name database duplication are often harmless for simple demo systems.
• PSF warnings about missing angles, dihedrals, or impropers are expected for the tiny demo topology.
• If Reset clears the preview, click Render; if the file still does not load, check format compatibility.
• If a trajectory is slow or fails, stride it, strip solvent, or upload a smaller test segment first.
• If GIF export finishes but you cannot find the movie, open the job output/download section and look for vmdweb-trajectory.gif.

Acknowledgements And Validation

• VMDWeb uses VMD for backend trajectory analysis and NGL Viewer for browser preview.
• ChemistryAtlas adds upload orchestration, generated Tcl scripts, sample files, browser animation, and job artifact downloads.
• Validate trajectory analysis against prepared MD files, simulation metadata, force-field assumptions, and independent analysis scripts before publication.