When running molecular simulations, especially with systems involving complex interactions or assembled components, one common challenge is controlling the movement of specific parts. For example, if you’re simulating a nanorobotic gripper, a poorly configured simulation might result in the gripper moving too quickly or in the wrong direction, leading to unexpected behavior like missed grips or structural instability.
The Simulate animation in SAMSON provides a helpful way to address this by combining it with other animation effects that control atomic positions. This allows you to perform constrained simulations more effectively, ensuring your systems behave as intended throughout each step of your animation.
Why Constraints Matter
Simulations calculate molecular motion based on physical principles, but sometimes we want to restrict how parts move—for instance, keeping a receptor still while a ligand binds, or slowing down the motion of a nanodevice component. Without constraints, the system might evolve in a physically valid but undesired direction, especially when component movements happen too rapidly between animation frames.
In the example shown on the same documentation page, the actuated arm of a nanogripper (in blue) moves down too quickly (1.7 nm over 2.5 ps, or 680 m/s), resulting in a failure to grasp the target cylinder. These types of missteps can be costly in design iteration and frustrating to debug without a targeted approach to simulation control.
Combining Animations in the Animator
In SAMSON, the Animator allows you to stack animation effects, executed in top-down order. You can first place animations that position atoms where you want them to be, and then add the Simulate effect to apply a simulation on the resulting arrangement. This ensures the simulation starts from your intended configuration, not from where the last unplanned motion may have left it.
To do this, double-click on the Simulate animation in the Animation panel. Drag the keyframe to ensure it happens after all the other keyframes that set your atomic positions. You can always reposition or edit keyframes later if adjustments are necessary.
Customizing Simulation Parameters
Once the Simulate animation has been added, you can fine-tune parameters directly within the Inspector. Two particularly useful settings are:
- Steps per frame: the number of simulation steps performed for every frame of animation.
- Step size: the integration timestep, controlling how finely the system evolves over time.
Carefully adjusting these helps avoid abrupt transitions that could destabilize your molecular system or lead to unrealistic outcomes.
Saving Motion Paths
To record the molecular trajectory generated by your constrained simulation, combine the Simulate animation with the Record path animation. This saves the entire motion path and makes it easier to visualize system behavior later—or even replay it in reverse using the Play reverse path animation effect.
For more details, see the full documentation page 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.