If you’ve ever needed to simulate the same molecular system under multiple conformations — for example, in Umbrella Sampling or conformational ensemble simulations — then you probably know how time-consuming it can be to prepare each conformation manually.
Good news: the GROMACS Wizard Extension in SAMSON makes it possible to set up and run batch computations for many conformations in one go. This post breaks down how to do it, using either a single trajectory or a set of conformations as input.
What’s the problem?
Molecular modelers often have one system — e.g., a protein-ligand complex — with many different starting conformations. These may come from:
- Trajectories from Molecular Dynamics (MD)
- Normal Modes analysis
- Docking tools
- Custom generated paths or animations
But setting up MD simulations for each conformation manually is tedious and error-prone. What’s needed is a way to automate this.
Enter: Batch preparation in GROMACS Wizard 💡
SAMSON’s GROMACS Wizard allows users to create a batch project that contains all the conformations or trajectory frames as subprojects. From there, you can minimize, equilibrate, and simulate everything in batch — either locally or in the cloud.
Step-by-step overview:
- Load your trajectory or conformations into SAMSON (drag-and-drop or
Home > File > Open). - Open the Prepare tab in the GROMACS Wizard.
- Select your molecular system in the Document View and set it as the system.
- Check the box: [Optional] Batch preparation.
- Select your conformations or path (trajectory).
- Click the Set conformations or a path button. This gives visual control over the conformations thanks to a slider.
- Complete Step 1 of the GROMACS Wizard: Choose force field, solvent, and optionally, custom index groups or ions.
- Define the periodic box:
- Box lengths: Uniform box for all conformations (based on largest size)
- Solute-box distance: Individual box per conformation (e.g., 1 nm spacing)
- Click Prepare. SAMSON generates one folder per conformation, all ready for simulations.
Simulation: All at once
Once the batch is prepared, you can run:
Select the input source as From batch folder, and all conformations will be processed sequentially, each as its own job.
Where to monitor progress
Whether you are running jobs locally or on the cloud, each conformation gets assigned its own job. You can track them from:
- Local Jobs panel for jobs running on your machine
- Cloud Jobs panel for remote submissions
Why this matters
This workflow removes the repetitive manual effort usually required to set up GROMACS simulations for many input states. It’s especially beneficial when working with ensembles or doing sampling that requires dozens — or hundreds — of conformations.
To learn more, visit the full documentation page: Batch Computations with GROMACS Wizard.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.