Exploring molecular dynamics for flexible systems often involves analyzing multiple conformations or frames of a molecular system. If you’ve felt the pain of having to simulate each conformation separately — with endless copy-pasting, configuration, and rerunning — you’re not alone. Managing dozens or even hundreds of similar simulation jobs can quickly become overwhelming, especially when trying to ensure consistency in simulation parameters.
Luckily, SAMSON’s GROMACS Wizard offers an integrated and streamlined way to handle batch simulations, enabling molecular modelers to minimize, equilibrate, and simulate multiple conformations — all from a single trajectory or path — in a single workflow.
Why simulate conformational ensembles?
Running simulations on just one conformation often gives you a limited picture. In real biological environments, molecules like proteins, ligands, and complexes sample a wide range of conformations. Whether you’re exploring Umbrella Sampling, testing the robustness of binding or just studying system dynamics under thermal fluctuations, simulating multiple conformations makes your results more comprehensive.
From Trajectory to Batch Simulations
Using SAMSON, you can start by importing or generating a trajectory. Open it via Home > File > Open (or use Ctrl / Cmd + O), or simply drag and drop it into the interface. Next, select specific frames or export all as conformations — these will serve as your entry points in the batch simulation pipeline.
Selecting key frames
Use the Inspector to browse trajectory frames and manually export conformations. Alternatively, convert the whole trajectory to a set of conformations using the context menu: Path > Create conformations from path, then keep only the ones you need.
Setting Up a Batch Project
Once you have your conformations:
- Go to the Prepare tab of the GROMACS Wizard.
- Select your system from the Document View and mark it as your molecular system.
- Check the Batch Preparation option.
- Select multiple conformations or a trajectory path. Choose either:
- A set of conformations – each one becomes a subproject
- A path – each frame becomes a subproject
- Set your force field, solvent model, periodic box definition, and other preparation parameters.
- Click Prepare – a new batch project with separate folders will be created, one per subproject.
Defining the Periodic Box
This step deserves special attention: when dealing with multiple conformations, box size becomes nontrivial. You can define boxes either:
- Once for all conformations (option: Box lengths)
- Individually per conformation (option: Solute-box distance)
The latter often yields advantages in simulation time for more compact conformations, while the former ensures uniformity across the batch.
Launching the Simulations
After preparation, run the standard steps for each subproject in the batch:
Each batch can be launched locally or in the Cloud — depending on your compute resources. SAMSON handles queuing of jobs per subfolder, lets you monitor status, cancel or reprioritize tasks, and imports results effortlessly.
To learn more, read the full documentation here: GROMACS Wizard – Batch Computations.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at www.samson-connect.net.