Studies
The studies in your workspace.
Config Builder
Configure a new MD simulation and analysis
Saved in this browser
1
Start
Or describe the study to the Agent
Start from an example
Systems
Every system runs with the settings below. Settings for one system only are listed on its row.
Trajectory
Structure
The structure describing the atoms the trajectory moves; found beside it where it can be.
Config file
Results folder
What runs
2
System
How the structure becomes the system that is simulated3
Protocol
How long, under what conditions, and how many runs4
Analysis and report
The same themes as the Analysis page5
Review
Nothing running
Running until it is determined
runningEach round
What would fix it
What the analyses determined
Simulation health
—
Live health classification will appear once telemetry has been written.
The run
Open the viewer
Waiting for a structure file…
The newest frame, as it is written.
- Production
- —
- Frames written
- —
- Atoms
- —
- Platform
- —
- Wall time
- —
- Checkpoint
- —
- Last update
- —
Live charts
Potential energy (kJ/mol)
—
Total energy (kJ/mol)
—
Temperature (K)
—
Density (g/mL)
—
Simulation speed (ns/day, derived)
—
equilibration, before 0 · each axis fits the production; what lies beyond it is marked at the edge
Live telemetry will appear after the first sample.
Methods
Molecular Viewer
Live molecular canvas, ligand tools, trajectory playback
Sequence
Waiting for structure
The 3D viewer will initialize when a topology or prepared PDB becomes available.
Playback
What holds the ligand
Analysis
Trajectory analyses and protein-ligand interactions
no analyses yet
Download all SVG figures
What the analyses determined
| Analysis | Mean ± standard error | Frames averaged | Independent samples | Status |
|---|
No analysis matches. Clear the filter to see them all.
Runs compared
Analysis outputs not available yet
Analyses and reports appear here after the analysis/report phases run.
Re-running analyses will appear without restarting the dashboard.
Report
The study, written up.
No report yet. The report phase writes one at the end of a run.
Files
Everything the study wrote, in the order it ran
Reading the study's files…
Agent
Describe a study, or ask about the one open.
What would you like to study?
I draft a config and the software validates it. Nothing runs until you say so.
I am not set up yet. Until then, I answer the questions about this study from its records.
About this study
Start a study