Feature Request

Problem / Motivation

When molecules are flexible, the alignment of molecules by using the local axes in each frame is not perfect and this causes force correlations to be lost in the averaging.

Proposed Solution

For molecules where there are N flexible dihedrals, the N largest eigenvalues should be multiplied by 0.25 before the vibrational entropy is calculated (this is equivalent to halving the forces).
Flexible dihedrals are defined as dihedrals with more than one peak in the dihedral histogram.

Expected Impact

• There will need to be counting of flexible dihedrals and this will fit in with the dihedral analysis currently being done for the conformational entropy.
• This will then create a link between the confromational state preparation step and the vibrational entropy calculation step.