Molecular simulations often involve exploring the effect of different conformations of the same molecule. Whether you’re running umbrella sampling experiments or simply want to assess the stability of alternative poses, preparing the simulation for each conformation manually can be repetitive and time-consuming. This is where SAMSON’s GROMACS Wizard batch preparation for conformations becomes a helpful timesaver.
In this post, we’ll focus on how to use SAMSON to set up GROMACS-ready projects for a single molecular system with multiple initial conformations using batch mode. No need to manually configure simulations for each structure—this feature lets you prepare them all at once, whether you’re running locally or in the cloud.
Why simulate multiple conformations?
- To explore conformational stability of a ligand or protein
- To perform ensemble-based simulations starting from diverse structural states
- To set up umbrella sampling or other advanced protocols requiring numerous initial poses
Step-by-step: Preparing multiple conformations for GROMACS with SAMSON
Before you begin, load or create a trajectory or a set of conformations in SAMSON. You can either:
- Load a trajectory (e.g., from MD): drag and drop it or use Home > File > Open
- Manually define conformations: use tools like Twister, motion animations, or analysis extensions like AutoDock Vina Extended or Normal Modes Analysis
If you’re only interested in certain frames of your trajectory, you can export just those frames into discrete conformations for batch processing. Use Edit > Conformation from the Inspector for specific frames or convert the entire path and remove the unwanted ones later.
Batch preparation workflow
- Open the GROMACS Wizard and switch to the Prepare tab.
- Select the molecular system in the Document view.
- Enable the Batch preparation checkbox.
- Select either:
- A set of conformations
- Or a trajectory (path)
- Click Set conformations or a path.
- Choose model, force field, solvent, and define ions and (optional) index groups.
- Define the periodic box:
- Box lengths – same box for all conformations.
- Solute-box distance – box calculated per conformation (minimum 1 nm recommended).
Use the batch preview slider to inspect how the box fits different structures.
- Click Prepare to generate one project folder for each conformation.
What’s next?
This batch setup ensures that you can apply the same simulation conditions to all your conformations efficiently. Each subfolder acts as a complete project, ready for energy minimization, equilibration, or production MD runs. You can even run these simulations directly in the cloud from SAMSON if you prefer not to rely on local resources.
By using conformational batch processing, you’re not just saving time—you’re enabling more statistically robust and diverse simulation outcomes.
To learn more, visit the full documentation page for this feature: Batch Computations with GROMACS Wizard.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.