Dynamics

Except regular design features, Catana also provides "dynamics" functionality (available via Dynamics menu in Top bar). Dynamics is a term we use for features offering possibilities of structural adjustment and feedback, based on underlying computations.

Rigid body dynamics

The purpose of rigid body dynamics is to fix unnaturally long phosphodiester bonds of coarse-grained DNA structures.
The computation first clusters DNA nucleotides and then runs rigid body physics simulation moving the clusters around.

Relaxation

Relaxation functionality allows for starting a molecular dynamics relaxation of all-atom and coarse-grained strucures using the GROMACS package.

Real-time collision detection

Collision detection suite employs WebGPU technology to visualize locations where individual structures collide with each other.
This is especially useful during structural assembly, as it helps to avoid sterical clashes, causing problems later in the simulation pipeline.

View trajectory

This feature enables to examine MD trajectories, either by using automatic playback or in step-by-step manner. Moreover, the trajectory frames can also serve as a basis for a creation of new structures – using just a single button click.