Setting up molecular dynamics (MD) simulations is often time-consuming, especially when you need to run many initial conformations of the same molecular system. For example, you might want to test different ligand poses, protein conformations, or results from docking, normal mode perturbations, or pathway generation. Doing this manually multiplies the setup time, increases the chance of mistakes, and makes large-scale exploration harder. Fortunately, the GROMACS Wizard in SAMSON provides a solution: batch simulations ⭐.
This blog post covers how to prepare and launch a batch of GROMACS simulations using conformational paths or a set of conformations in SAMSON. This streamlined process is especially helpful for molecular modelers working on docking studies, sampling different initial conditions, or studying protein flexibility.
🔄 From Trajectories to Simulations
To begin, you need a path or a set of conformations loaded in SAMSON. These can come from different sources:
- Dynamic simulations or animations (Dock/Undock, Move, etc.)
- Extensions like Normal Modes Analysis, docking modules, or Ligand Path Finder
- Manual editing with Move editors or Twister
If you do not want to use all trajectory frames, you can create conformations from specific frames using:
- Edit > Conformation from the Inspector for selected frames
- Create conformations from path to generate all, then delete the ones you don’t need
💼 Preparing Your Batch Project
Once you have your conformations ready, open the Prepare tab in the GROMACS Wizard and enable the batch project box:
- Select either a set of conformations or a path
- Use the slider to preview each initial state
- Each subfolder in the batch corresponds to an individual simulation project
Batch preparation allows you to set force fields, solvation, ions, and the periodic box setup in one go.
📦 Handling the Periodic Box
There are two approaches:
- Box lengths – simulate with the same box for all conformations
- Solute-box distance – setup a custom box per conformation; saves resources when conformations differ significantly in size
Visualizing the periodic box setup is easy with the built-in slider, helping you detect if your system fits comfortably within the box and complies with the minimum image convention.
⚙️ Running the Simulations
You can now proceed through standard GROMACS steps for each batch member:
- Energy minimization
- NVT/NPT equilibration
- Production Molecular Dynamics
Click the 
button to automatically select the batch project as simulation input.
📡 Local vs Cloud Execution
GROMACS Wizard lets you run simulations either locally or in the cloud:
- Locally: launch all subprojects as individual jobs and monitor them through the Local Jobs window
- Cloud: offload computation if your local setup is limited
Why It Matters
Running multiple simulations in parallel is a common requirement in computational drug design and structural biology. Whether improving reproducibility or testing conditions efficiently, batch projects help you:
- Reduce repetitive work
- Ensure consistency across simulation setups
- Scale easily for high-throughput analysis
Explore all the details in the original documentation page: Batch Computations with GROMACS Wizard
SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON at https://www.samson-connect.net.