One of the common challenges in molecular modeling is ensuring that a newly created structure is physically realistic. Molecules built manually or imported from other software often start in high-energy, non-equilibrium configurations. This can distort simulations and affect downstream analyses like docking or property prediction.
A fast and intuitive way to resolve this is to perform molecular geometry optimization directly within the SAMSON platform, using interactive simulations.
Why Interactive Optimization?
Unlike batch simulations that require submitting a job and waiting for results, interactive simulations in SAMSON let you observe and influence the molecule in real-time. You can nudge atoms, watch how the structure responds, and immediately see the effect of force fields and integration schemes.
Setting Up a Simulation
To run a geometry optimization, you need to create a simulation node that combines:
- An interaction model (force field), such as the Universal Force Field (UFF)
- A state updater, which defines how the system evolves, like Interactive modeling or the FIRE Integrator
- A dynamical model that holds the system’s degrees of freedom
You can add a simulator in SAMSON via Edit > Add simulator or using the shortcut Ctrl+Shift+M.
Walkthrough: From Structure to Optimized Geometry
Here’s what a typical interactive optimization workflow looks like in SAMSON:
- Build or import a molecule
- Add a simulator node: specify the interaction model (e.g., UFF) and the state updater (e.g., Interactive modeling)
- Start the simulation:
Edit > Start simulationor press X on your keyboard - Observe or guide the molecule: drag atoms to see how the structure reacts and settles into a more stable shape
This interaction is especially useful when modeling flexible systems or optimizing pieces of a larger structure.
For enhanced control, you can modify simulation parameters such as the number of steps and the step size in the state updater. Increasing these values allows for smoother convergence to a stable configuration.
Quick Example: Flattening a Carbon Nanotube
As illustrated in the video below, a sliced carbon nanotube quickly relaxes into a nearly planar graphene sheet when using the FIRE integrator:
Accessing and Tracking Conformations
Each optimized structure can be stored as a conformation—a snapshot of atom positions. These can be saved via Edit > Conformation or by pressing S. You can restore previous conformations or animate trajectories by connecting multiple conformations into a path.
Interested?
If you’re frequently tweaking molecular geometries and need immediate visual feedback, SAMSON’s interactive simulation functionality offers a streamlined and highly visual solution. It helps reduce structural artifacts and improves realism before proceeding to more complex simulations or analyses.
To learn more, visit the full documentation page here: SAMSON – Modeling and Simulation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.