Molecular simulations often require running the same protocol for multiple initial states. Whether you’re performing Umbrella Sampling, exploring conformational variability, or evaluating system responses, you likely need to simulate not just one, but many conformations of the same molecule.
This workflow, while essential, can be tedious to manage manually: importing frames, setting up input files for each, building boxes, selecting parameters, and launching the same simulation protocol again and again.
Using the GROMACS Wizard in SAMSON, you can automate simulations across multiple conformations from a single trajectory — without scripting. Here’s how you can streamline this process.
Why use trajectory frames?
Trajectories store the dynamic behavior of molecular systems. Rather than starting from a static structure, you can launch simulations from key frames in a trajectory to:
- Explore transition states
- Perform ensemble simulations for statistical mechanics
- Identify conformation-dependent properties
With SAMSON, you can easily export conformations from a trajectory and use them as starting points for simulations — all within an interactive interface.
Step-by-Step Overview
First, import your molecular trajectory using Home > File > Open or by drag-and-drop. You can also generate trajectories directly in SAMSON using various extensions like AutoDock Vina Extended or Normal Mode Analysis.
If you only want to use selected frames, SAMSON offers tools to create conformations for specific frames:
- Navigate the trajectory via the Inspector panel.
- Use Edit > Conformation to extract the current frame.
- Alternatively, create conformations from the entire path via Path > Create conformations from path, then delete those you don’t need.
Batch Preparation
Once you have your selected conformations:
- Open the GROMACS Wizard and go to the Prepare tab.
- Select the system and enable the [Optional] Batch preparation checkbox.
- Select conformations or a path in the Document view — each becomes a subproject.
- Click Set conformations or a path and verify your selection.
- Define your force field, solvent, ions, and optionally add custom index groups.
- Set the periodic box once for all conformations or individually per frame, depending on your needs.
- Click Prepare.
Each conformation becomes a separate project inside a batch folder, fully configured and ready for simulation.
Launching Simulations
Once the systems are prepared, processing the entire batch—minimization, equilibration, production—is simple. Use the same GROMACS Wizard steps as for a single system, selecting the From batch folder option when prompted.
Computations can run locally or in the Cloud. Each subfolder runs independently — allowing you to monitor progress or prioritize important conformations without restarting the full batch.
See how the periodic box fits
Use the slider in the Batch preparation box to visually inspect how the periodic box fits around each conformation. This is particularly useful if you’re working with diverse structural states.
A scalable way to explore molecular diversity
This workflow helps eliminate repetitive setup tasks and reduces the risk of user error. It’s a great way to perform high-throughput simulations from a conformational ensemble — without writing or maintaining scripts.
To explore more about batch simulations with SAMSON and the GROMACS Wizard, visit the full documentation: Batch computations with GROMACS Wizard.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.