CGeNArateWeb Help - Analysis Elastic Energy

Elastic Energy

The elastic energy $E_{bonded}$ of the DNA fiber in the current implementation is calculated following the CGeNArate model:

$$E_{bonded} = \sum_{a=2}^4 K_a(l-l_0)^a, \sum_{a=2}^4 K_a(\alpha-\alpha _0)^a,$$

$K_a$ are the interaction strengt constants for all unique tetrameric environments as derived from ABC microsecond-long MD simulations with the parmbsc1 force-field, $l_0, \alpha_0$ are the derived equilibrium distances and angles of the interactions, and $l, \alpha$ are these distances and angles measured throughout the trajectory.

Elastic energy of DNA: The table shows mean and standard deviation for the elastic energy of the DNA fiber as well as the average elastic energy per base pair

Elastic energy of DNA along trajectory (available for Trajectory Flexibility Analysis)

The elastic energy and the average elastic energy per base pair (y-axis, in kcal/mol) is shown for each snapshot (x-axis) of the trajectory: