When modeling nanosystems, researchers frequently face the challenge of keeping parts of the system fixed or following a pre-defined motion, while letting others evolve naturally according to physical laws. This is often the case when simulating mechanical systems like molecular machines, protein conformational changes with fixed anchors, or designed nanogrippers in motion.
In SAMSON, the Simulate animation helps address this challenge by performing a multiple-step physical simulation at each animation frame. But its real power lies in its ability to work in combination with other animations that dictate atomic positions, enabling constrained simulations.
Why constrain simulations?
Imagine you are modeling a nanorobotic arm that must follow a precise path or respond to an actuator. Simply running a full simulation may not preserve that path due to thermal fluctuations or unrealistic motions. In contrast, combining controlled motion with a physical simulation allows you to model more realistic, functional behaviors while keeping user-defined constraints—invaluable for design and analysis.
How to do this in SAMSON
To implement this, insert the Simulate animation after other animations that control atomic positions, such as custom motion or path playback. SAMSON’s Animator executes animations from top to bottom, so ordering matters. This ensures that atoms first follow the intended motion, and then physical simulation updates are applied accordingly.
You can add the Simulate animation by double-clicking it in the Animation panel. A keyframe is placed at the current frame, and it can be moved as needed to synchronize with other motions.
Tuning simulation dynamics
If the motion looks too fast or unstable, you may need to adjust how many simulation steps are performed per frame or change the step size. You can do this directly in the Inspector for the Simulate animation. Increase the number of steps per frame or reduce the step size to make the simulation smoother and more accurate, especially in systems with strong forces or high-speed motions.
Example: a nanogripper that misses
In a real-world example, a nanogripper was simulated with motion applied to a moving ‘blue’ part. The speed was too high—about 680 m/s—causing the gripper to miss the target cylinder. This illustrates how combining motion and simulation reveals critical insights early in a system’s design.
This hybrid strategy bridges the gap between animation and physics, providing actionable feedback. You can experiment freely without writing complex code, ensuring both control and realism in your molecular system modeling.
To learn more about simulating with constraints in SAMSON, and see additional examples, refer to the official documentation here: https://documentation.samson-connect.net/users/latest/animations/simulate/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.