One of the most frustrating issues for molecular modelers is running a simulation only to realize afterward that the initial positions of atoms weren’t quite right. The result? Drifting atoms, broken structures, or failed mechanical behavior. If you’ve ever tried simulating nanodevices or molecular machines, you’re probably familiar with these headaches.
That’s where combining animations in SAMSON becomes particularly useful. In this post, we’ll talk about how to perform a constrained simulation using the Simulate animation in SAMSON, in combination with other animations that define initial atomic positions. Whether you’re controlling atomic displacements manually or scripting behavior, SAMSON gives you layered control over molecular simulations.
Why constrained simulation matters
In many molecular design tasks, you want to simulate how a structure behaves over time, but you also want to ensure that it starts from the correct geometry or configuration. For example, you might want a nanogripper to close around an object smoothly instead of falling apart because it was misaligned.
This is a common use case when animations update atomic positions at specific frames. However, if a simulation starts before these initial positions are set, the simulation’s results can be meaningless or misleading.
Controlling execution order
SAMSON’s Animator panel executes animations from top to bottom. If you’re layering multiple animations—such as atom movements followed by a simulation—it is crucial to place the Simulate animation after those that set up the environment. This ensures that each simulation frame uses the latest geometry coming from the other animations.
Tip: You can easily rearrange animation keyframes and effects in the Animator to control when and how they affect your system.
Fine-tuning simulation parameters
Once added, the Simulate animation allows configuration through SAMSON’s Inspector. You can change:
- Steps per frame: How many simulation steps will be performed at each animation frame.
- Step size: Fine control over the resolution of each step taken by the simulation.
This enables users to simulate faster or slower processes depending on system dynamics. For example, increasing the number of steps per frame may lead to smoother dynamic visualizations, which is especially helpful when evaluating interaction geometries or mechanical behaviors.
Practical example: Why timing matters
A real-world use case was shared on Twitter by Stéphane Redon, where a nano gripper fails to grasp a cylinder because the actuated part moves too fast (1.7 nm in 2.5 ps—about 680 m/s). This type of mechanical failure can result from misconfigured simulation timing or missing constraints. Ensuring proper setup through layered animations and controlled velocities can prevent such failures and lead to more reliable design insights.
Simulating nanosystems helps designing them. In this example, the actuated part (in blue) of the nano gripper moves down too fast (1.7nm over 2.5ps -> 680m/s) and the gripper fails to grasp the cylinder. (Gripper design by @mooreth42, who showed a successful grasp at a different… pic.twitter.com/M5yKD7uA8T
— Stephane Redon (@StephaneRedon) May 8, 2024
Saving and analyzing the results
If you want to study the dynamics after simulation, don’t forget to use the Record path animation. It captures the full trajectory resulting from your configured simulation and is compatible with playback tools like Play path and Play reverse path.
To dive into more technical details and implementation steps, you can visit the full documentation here:
https://documentation.samson-connect.net/users/latest/animations/simulate/
SAMSON and all SAMSON Extensions are free for non-commercial use. Download SAMSON at https://www.samson-connect.net