Simulating nanosystems can provide valuable insights for designing molecular structures, but a common issue faced by molecular modelers is the lack of control over atomic trajectories during simulation. When molecules don’t behave as intended—like moving too fast or too far—this can lead to unrealistic results or even complete failure of the modeling goals, such as failing to dock, fold, or grasp a target.
This is especially important in simulations involving mechanical motion, for instance when modeling nano-grippers, motors, or molecular machines. A typical challenge: how can one test such a mechanism while ensuring that atoms or substructures remain on a planned path?
Why Use Constrained Simulations?
In real-world experiments, scientists use jigs, motors, or external fields to control the positions of nanoscale structures. In molecular modeling, a similar approach makes sense: combining free simulations with constraints can help achieve simulations that are both physically realistic and functionally purposeful.
This is where the Simulate animation in SAMSON becomes valuable. It enables simulations where each frame executes multiple simulation steps—but what makes it even more useful is how it can be combined with other position-controlling animations for constrained simulations.
Layering Simulate with Path-Controlling Animations
To perform a constrained simulation, you can add the Simulate animation right after an animation that drives specific atomic motions (such as paths or transformations). The Animator in SAMSON executes animations sequentially from top to bottom, which means the position-setting animations should appear above Simulate in your animation stack.
This layering allows you to guide atoms to desired positions across frames while still simulating their motion dynamically. For example, a part of your structure can be forced along a vector direction, while still accounting for environmental and structural forces—simplifying things like loop closure or mechanical response analysis.
Customize Simulation Steps per Frame
Another flexibility provided by the Simulate animation is the ability to set how many simulation steps are performed per frame, as well as the step size. These parameters can be adjusted in the animation’s Inspector panel. If a simulation runs too quickly or fails to correctly follow physical constraints, reducing the step size or increasing the number of steps can help achieve more faithful behavior.
Real-World Example: Nano-Gripper Design
Take the case shared by molecular modeler @mooreth42. In a test simulation of a nano-gripper, the actuated part moved downward too quickly—covering 1.7nm in 2.5ps (about 680m/s)—resulting in a failed attempt to grasp a cylindrical object. While the design was mechanically sound, insufficient temporal resolution caused the gripper to miss its target. With proper constraints and step parameters, such failures can be avoided.
How to Add and Adjust the Animation
To use the animation in SAMSON:
- Double-click the Simulate animation in the Animation panel.
- Position its keyframe after those of animations that drive atom positions.
- Use the Inspector to adjust simulation parameters like the number of steps per frame and step size.
You can also use the Record path animation to capture the trajectories created by your constrained simulation and replay them using Play path or Play reverse path.
Conclusion
Combining the Simulate animation with path or position animations in SAMSON provides a flexible solution for constrained molecular simulations. Whether you’re modeling folding, docking, or mechanical interactions, controlling atomic motion while allowing for simulation feedback can greatly improve the realism and reliability of your designs.
To learn more about the Simulate animation, visit the official documentation: https://documentation.samson-connect.net/users/latest/animations/simulate/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON here: https://www.samson-connect.net