Setting up molecular dynamics (MD) simulations for a series of conformations can be a tedious task—especially when you want to explore how small differences in protein structure affect simulation outcomes. Manually preparing each conformation for simulation increases setup time and increases the chance of human error.
If you’ve ever wished you could just use frames from a trajectory as starting points for batch GROMACS computations—you’re in luck. The GROMACS Wizard in SAMSON lets you convert trajectory frames into separate subprojects, each ready for minimization, equilibration, and simulation. Here’s how this works and why it might save you hours of manual prep work.
Use a single trajectory to simulate multiple conformations
Let’s say you already have a trajectory—maybe the result of an earlier simulation or a set of conformations from an extension like AutoDock Vina Extended or a Normal Modes Analysis. In SAMSON, you can turn either the full trajectory (or just a few selected frames) into a batch of independent MD simulations. This is helpful if you want to explore how slight variations affect energy landscapes, binding behavior, or conformational transitions.
Start from your trajectory
Begin by loading your trajectory via Home > File > Open (or drag and drop). If you’d like to select specific frames instead of using them all, you can:
- Use the Inspector to browse frames and create conformations via Edit > Conformation.
- Or, create conformations from the entire trajectory path (right-click on the path node > Path > Create conformations from path) and delete the ones you don’t need.
Set up batch preparation
- In the GROMACS Wizard, go to the Prepare tab.
- Select your molecular system model and check the [Optional] Batch preparation box.
- Select either:
- A path: each trajectory frame becomes a subproject.
- A set of conformations: each conformation becomes a subproject.
- Click Set conformations or a path. You’ll see the conformation count and can preview them via a slider.
From here, you can choose a force field, solvent type, add custom index groups, and specify ions—just as you would in any regular setup.
Choosing the periodic box
SAMSON gives you two options for defining the periodic box during batch setup:
- Box lengths: Use the same box size across all conformations, based on the largest dimensions.
- Solute-box distance: Define separate boxes per conformation. This can cut down computation time for compact structures.
The visual slider in SAMSON lets you confirm that each conformation fits properly within the defined box size.
Why this helps
This approach simplifies workflows like Umbrella Sampling, conformational scanning, or studies with flexible ligands and proteins. It pushes you closer to batch simulation workflows typically used by large platforms, but without scripting or diving into file formats.
Want to see the bigger picture? Check out the full documentation on batch computations here.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.