Description
When constructing an elastic network (EN) of a biomolecule, the resulting network can be non-rigid, i.e. containing floppy modes.
This issue can be solved by increasing the cut-off distance of the EN.
Unfortunately, we only find about the network's rigidity postfactum, after Hessian matrix decomposition has occurred which is the most computationally expensive step in the elastic network model (ENM) construction.
Figure Rigidity of two 2D structures. Top Square is not rigid. The deformation results in a shear mode. Bottom Triangle is rigid!
For the 2D structures, we can construct a Laman graph that will produce a rigid network. However, this approach fails in 3D space.
References
Description
When constructing an elastic network (EN) of a biomolecule, the resulting network can be non-rigid, i.e. containing floppy modes.
This issue can be solved by increasing the cut-off distance of the EN.
Unfortunately, we only find about the network's rigidity postfactum, after Hessian matrix decomposition has occurred which is the most computationally expensive step in the elastic network model (ENM) construction.
Figure Rigidity of two 2D structures. Top Square is not rigid. The deformation results in a shear mode. Bottom Triangle is rigid!
For the 2D structures, we can construct a Laman graph that will produce a rigid network. However, this approach fails in 3D space.
References