One of the common challenges in molecular simulations is running the same GROMACS workflow (minimization, equilibration, simulation) across multiple conformations of the same molecular system. Whether you’re performing an Umbrella Sampling study or simply exploring the conformational landscape, repeating the setup process frame by frame is tedious and error-prone.
The GROMACS Wizard in SAMSON solves this problem neatly by allowing you to prepare all conformations for simulation at once — using batch projects. This functionality can dramatically speed up your workflow and ensures consistent simulation parameters across all samples.
When is batch preparation useful?
Imagine you’ve generated a trajectory from normal mode analysis, docking animations, or protein-ligand interaction simulations. You now want to simulate each frame under the same molecular dynamics protocol.
Traditionally, this would mean preparing each conformation separately, repeating steps like solvation, ion setup, and defining periodic boxes. With batch preparation, it’s all handled in one go.
How it works in SAMSON
After creating or importing a trajectory into SAMSON, you can launch the batch preparation by going to the Prepare tab in the GROMACS Wizard and checking the “Batch preparation” box. Then:
- Choose the structural model you’ll apply to all conformations.
- Select the trajectory (path) or a set of specific conformations to be used as initial states.
- Click Set conformations or a path, and they’ll be linked to subprojects.
- Configure the simulation model: choose force fields and solvent, define box settings, and specify ion parameters.
- Use the Prepare button to generate a batch project with all systems ready for the next steps.
Each conformation becomes a separate subproject, and you can proceed with minimization, equilibration, and simulation either locally or on the Cloud.
Two ways to control box sizes
The batch setup offers two options to define the periodic box:
- Box lengths: Determines a single box for all conformations.
- Solute-box distance: Computes a unique box per conformation — smaller boxes for compact frames can reduce computational time.
You can visualize how the box fits each frame using the built-in slider tool.
Why this matters
Automating this process reduces not only the time spent but also inconsistencies introduced by manual interventions. If you’re running dozens or hundreds of simulations — such as per-frame free energy calculations or a large-scale conformational survey — this can make a significant difference.
To learn more or walk through each step in detail, visit the full documentation page here.
SAMSON and all SAMSON Extensions are free for non-commercial use. To get started, download SAMSON from https://www.samson-connect.net.