Simulating Multiple Conformations at Once: A Time-Saving Workflow for Molecular Modelers

One of the recurring challenges in molecular modeling is evaluating how different conformations of a single molecular system behave under identical simulation conditions. Whether you’re performing Umbrella Sampling or exploring conformational variability, setting up individual simulations for each structure can be tedious and error-prone.

If you’re using SAMSON and GROMACS Wizard, there’s a more efficient way: batch preparation of multiple conformations from a trajectory or set of conformers.

When Would You Want This?

If you have a single system — such as a protein — but want to simulate it across many conformations (e.g., from a molecular dynamics trajectory, normal mode perturbations, or docking poses), you can automate the setup for all of them. Instead of preparing each structure one at a time, batch preparation generates ready-to-run subprojects for each conformation quickly.

Getting Started: Importing Trajectories or Conformations

You can begin by:

  • Loading a trajectory into SAMSON via Home > File > Open or drag-and-drop.
  • Using SAMSON tools or extensions to generate conformations (e.g., Twister, Ligand Path Finder, Normal Mode Analysis).

Need conformations from specific frames only? You can:

  • Select frames manually via the Inspector and convert them into conformations.
  • Create all conformations from a path and then delete the ones you don’t need.

Step-by-Step: Batch Preparation

  1. Open the Prepare tab in the GROMACS Wizard.
  2. Select the molecular system from the Document view.
  3. Check the Batch preparation box.
  4. Select either:
    • A set of conformations
    • A single trajectory (each frame becomes a separate subproject)
  5. Click the Set conformations or a path button. Use the slider to preview them.
  6. Choose parameters such as force field, solvent, optional custom index groups, and ions.
  7. Define the periodic box:
    • Box lengths: Same box for all conformations.
    • Solute-box distance: Unique box per conformation (recommended at least 1 nm for each).
  8. Click Prepare. Each conformation now has its own project folder.

Why It Matters

This feature eliminates repetitive manual work and reduces the chance of errors. If you’re planning to run identical simulation conditions (minimization, equilibration, MD production) across several conformers, this approach will save significant time. You can move from setup to simulation with minimal overhead.

Visual Tip

After defining the periodic box, use the slider in the Batch preparation box to visually check how each conformation fits in its box. This helps avoid issues due to insufficient box size.

Input source type

Next Steps: Simulation

With your batch project ready, proceed as usual:

  • Minimize
  • Equilibrate (NVT and NPT)
  • Run production MD

Select From batch folder as input. You can run locally or in the cloud, and each subfolder launches its own job.

Learn more in the official documentation.

SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.

Comments are closed.