[gmx-users] [EXTERNAL] Re: Measuring bond distances, angles and dihedrals

[Yu Du]

Hi Micholas,
Also a word of warning for the original suggestion of using VMD. Two words of caution: 1) Be sure you unwrap your trajectories carefully before using vmd for the analysis (otherwise you may get odd 'spikes' in your distances due to the PBC), 2) Since vmd doesn't have any topology information, all of the bonds/angles/dihedral information is inferred, so make sure you are using your selections very carefully.
Yes, I really omitted the versatile tools that GROMACS have provided and heavily relied on VMD. VMD indeed needs a careful preprocess of trajectories and selection of atom set for correct and reliable analysis.

Thanks for your caveats.

Yu