Running simulations on a single molecular structure is common practice, but what if you have many starting conformations of the same molecule? Whether you’re studying flexibility, rare events, or preparing umbrella sampling, working with many initial conformations can quickly become tedious if done manually—especially when you need to set up identical parameters for each run.
If this sounds familiar, the GROMACS Wizard in SAMSON offers a way out. Its batch preparation mode lets you set up simulations from multiple conformations—all at once. You can then launch minimization, equilibration, and MD simulations either locally or in the cloud. Let’s walk through how it works and why it saves time.
📁 Load Trajectory or Conformations
You can drag and drop a trajectory into SAMSON, or use Home > File > Open (Ctrl/Cmd + O) to load an existing one. Alternatively, you can generate conformations within SAMSON using tools like Twister or AutoDock Vina Extended.
You can extract conformations from specific frames of a trajectory in two ways:
- Manually step through frames using Inspector and create conformations for selected ones.
- Select a path, right-click it in the Document view, and use Path > Create conformations from path to create conformations from all frames, then delete the ones you don’t need.
🔧 Set Up Batch Preparation
Once you have the conformations ready:
- Open the Prepare tab in GROMACS Wizard.
- Select your molecular system in the Document view and set it.
- Check [Optional] Batch preparation.
- Select your set of conformations or a trajectory path and click Set conformations or a path. You’ll see how many conformations are detected and can slide through them.
- Choose the model (force field and solvent), optionally add index groups, and specify ions as usual.
📦 Define the Periodic Box for All Conformations
A common challenge is defining a box that fits all conformations. The GROMACS Wizard offers two ways:
- Box lengths: Same box size for all conformations. Good for consistency, but may be large due to outliers.
- Solute-box distance: Box size adapts to each conformation. Efficient for compact systems.
You can preview how each conformation fits in its box using the slider—handy for spotting issues early.
🚀 Next Steps
Once your batch is prepared, you can run minimization, NVT and NPT equilibration, and production MD in batch mode. Each conformation becomes its own project folder, with results easily accessible in the Local jobs or Cloud jobs windows.
You’ll find this workflow particularly effective if you’re preparing ensemble simulations or evaluating different initial states systematically—it reduces human error and boosts productivity.
Learn more in the official documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.