Sample._gyration¶

Sample._gyration(data, region, dist, com, pos, pore_id)¶

This function calculates the gyration radius of molecules inside the pore.

All atoms are sampled each frame if they are inside the bounds of the pore minus an optional entry length on both sides.

Inside the pore the atom instances will be added to radial cylindric slices \(s_{r,j}-s_{r,j-1}\) and outside to rectangular slices \(s_{z,k}-s_{z,k-1}\) with pore radius \(s_{r,j}\) of radial slice \(j\) and length \(s_{z,k}\) of slice \(k\).

The gyration radius is calculated using

\[R_g=\left(\frac{\sum_i\|\boldsymbol{r}_i\|^2m_i}{\sum_im_i})\right)^{\frac{1}{2}}\]

with mass \(m_i\) and position \(\boldsymbol{r}_i\) of atom \(i\) with respect to the center of mass of the molecule.

Parameters:

datadictionary: Data dictionary containing bins for the pore interior and exterior
regionstring: Indicator wether molecule is inside or outside pore
distfloat: Distance of center of mass to pore surface area
comlist: Center of mass of current molecule
poslist: List of atom positions of current molecule