Simulating molecular systems is crucial for understanding their dynamics, behavior, and structural responses to external forces. However, in many research scenarios, you don’t just want to let everything move freely — you want control. For instance, you may need to restrict some atoms to follow a defined path while the rest of the system responds accordingly. This is where combining SAMSON’s animations, and in particular, the Simulate animation with external position controllers, becomes very useful.
What is a Constrained Simulation?
Constrained simulation refers to the technique of allowing certain atoms in a system to move in pre-defined ways during simulation. This is useful when designing or testing nanosystems — for example, guiding the arms of a nano-gripper while simulating how the environment reacts to their motion.
Instead of manually updating atom positions at every timestep (which would be very inefficient), you can use animation layers in SAMSON to drive some atoms, and let the Simulate animation run a simulation during each frame based on these constraints.
Combining Simulate with Position Animations
SAMSON allows for a layered animation model where effects are executed from top to bottom. This makes it possible to combine animations that control positions (such as those moving atoms along certain paths) with the Simulate animation that evolves the system physically.
To perform constrained simulations:
- Start by using other animations to define how certain atoms should move over time. This could be a trajectory manually defined, read from a file, or created using SAMSON’s animation tools.
- Then, add the Simulate animation effect by double-clicking it from the Animation panel. It places a keyframe at the current frame.
- Finally, make sure that the Simulate animation comes after the position-controlling animations in the animation stack. Since SAMSON executes animations from top down, this order ensures that the positions are updated before the simulation step runs.
Tuning the Simulation Steps
You can further fine-tune how the simulation behaves in each frame. For this, open the Inspector for the Simulate animation, where you can:
- Change the number of internal simulation steps per frame.
- Adjust the time step size for the simulation.
This flexibility is particularly useful for balancing speed vs. accuracy, and helps avoid situations like unstable trajectories or atoms moving too fast.
Why This Matters
Being able to constrain simulations allows for more precise modeling and the creation of reproducible, design-driven simulations. Whether you’re testing a concept for a nanoscale mechanistic system, or visualizing how specific drug interactions unfold under guided conditions, constrained simulations remove the need for hardcoded scripting or separate preprocessing.
This method is both visual and interactive, and accessible to non-expert users, which makes it a valuable tool for education, rapid prototyping, and hypothesis testing.
To learn more, visit the full documentation page for Simulate in SAMSON.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON here.