Avoid Repeating Yourself: Batch Preparing Molecular Simulations in SAMSON

One of the recurring challenges in molecular simulations is running the same workflow multiple times for a set of slightly different initial conformations. Whether you’re sampling alternative ligand binding poses, scanning mutations, or simply running simulations from different frames of an existing trajectory, duplicating the simulation setup manually is tedious, error-prone, and wastes valuable time.

The GROMACS Wizard in SAMSON makes it much easier by providing a Batch Preparation feature—ideal for preparing a large number of molecular simulations efficiently based on different conformations or paths.

Why consider batch preparation?

Imagine you’ve generated 20 different conformations for a ligand–protein complex. You want to run GROMACS simulations for each of them. Setting up 20 independent projects manually is clearly inefficient. With batch preparation, SAMSON allows you to generate a separate numerical simulation project for each conformation—all in one go.

How it works

To use batch preparation, you first need to load or generate a set of initial conformations or a path (trajectory) in SAMSON. You can:

  • Import an existing trajectory.
  • Use various editors like Move editors or Twister to generate pose variations.
  • Generate trajectories using other extensions like AutoDock Vina Extended, Normal Modes Analysis, or Protein Path Finder.
  • Convert animations (e.g., docking, undocking) into conformations or paths.

Once you have your conformations:

  1. Open the GROMACS Wizard in SAMSON.
  2. Switch to the Prepare tab.
  3. Check the [Optional] Batch project box.
  4. Use the Set conformations or a path button to add your initial states.

Each selected conformation or frame will now be treated as a starting point for an independent sub-project. These will be organized into numbered subfolders under a single batch project folder.

Consistent or adaptive box sizing

SAMSON gives two options for defining the simulation box in batch mode:

  • Same box for all: Fit the box to all conformations collectively. This works well when conformations occupy similar space.
  • Adaptive box per structure: Fit individual boxes per conformation, using a solute-box distance (minimum 1 nm is recommended).

Adaptive boxes may significantly reduce simulation cost for compact structures, while a common box ensures uniform system setup.

Batch preparation input

After preparation: Automate simulation

After batch preparation, you can run:

  • Energy minimization
  • NVT equilibration
  • NPT equilibration
  • Production molecular dynamics

Every subfolder behaves like an independent project. You can run the jobs:

  • Locally: Each sub-project becomes a local job that can be managed individually.
  • In the Cloud: Useful for high-throughput scenarios with many conformations.

Batch preparation removes redundancy, reduces human error, and keeps your simulation campaigns organized—making it easier to focus on analysis rather than setup.

To learn more about how to use the Batch Preparation feature in SAMSON’s GROMACS Wizard, visit the full documentation: Batch Computations with GROMACS Wizard.

SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON here.

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