Running molecular dynamics simulations on multiple conformations of the same molecule—whether to sample different initial states or to conduct techniques like Umbrella Sampling—can be necessary but very repetitive. If you’ve ever found yourself manually preparing each structure, adjusting box sizes, solvent environments, or ion parameters for each variant, you’re not alone.
The GROMACS Wizard in SAMSON offers a clean solution to that problem with its batch preparation tool, allowing you to efficiently set up a simulation workflow for multiple starting conformations of a single molecular system—without tedious repetition.
Why this matters
Let’s say you’ve generated several conformations of a protein-ligand complex from docking, a normal mode analysis, or a simulated trajectory. Traditionally, preparing each conformation as a separate simulation project would mean re-specifying system parameters over and over. More importantly, ensuring consistency across these project setups can become error-prone.
This is where batch preparation simplifies the process. All you need is a trajectory or a group of conformations, and with just a few clicks, you can set up consistent simulations for each state.
Quick workflow summary
Here’s how you can prepare multiple conformations in one shot:
- Load a trajectory or a set of conformations in SAMSON. You can either:
- Open a trajectory file via Home > File > Open.
- Or drag-and-drop it into the interface.
- Go to the Prepare tab in the GROMACS Wizard.
- Check the [Optional] Batch preparation box.
- Select the trajectory or the specific conformations you want to use as initial structures for simulation.
- Click Set conformations or a path, which turns them into subprojects.
Each conformation will now become a separate ready-to-run simulation project within a common batch folder.
Handling the simulation box 💡
A critical decision during setup is how to define the periodic box. The GROMACS Wizard gives you two options:
- Box lengths: Set a common size for all conformations. Useful when you want consistency across simulations.
- Solute-box distance: Define the solvent distance individually for each frame. This allows smaller boxes for compact structures—translating into faster computations.
Using the slider in the interface, you can visually inspect how your chosen box fits the molecule across different states—this is helpful to avoid overlaps or excessive solvent padding.
From preparation to production
Once you’ve completed the preparation stage, every conformation becomes its own folder in the batch. You can then proceed to minimize, equilibrate, and simulate them all at once—either on your local machine or in the Cloud.
Each of these simulation jobs can be independently tracked, paused, or analyzed. Yet everything starts from a consistent preparation step—minimizing setup error and saving significant time.
When to use this
This batch approach is especially helpful when:
- Working with conformational ensembles
- Sampling along a reaction coordinate
- Testing structural sensitivity to simulation parameters
- Using output from docking or normal mode analysis
For more information and a step-by-step guide, see the full documentation: Batch computations with the GROMACS Wizard.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON here.