[gmx-users] How do I monitor dynamics of helices and domain rotation?

[jayant james]

Hi all,

1) I am looking at see if two adjacent helices are changing their
conformation in space. I would like to monitor whether they are orthogonal
to each other or have become parallel to each other during simulations. Is
it possible in Gromacs to follow such changes, and if so, what command
would I use to track such changes?

2a) Also how would I track domain rotations? To check if a domain A is
rotating with respect to domain B. I am thinking of picking 2 amino acids
on domains A and B and monitor the dihederal angle to see if there is
rotation between domains A and B. Is it possible to do such an analysis
using Gromacs and if so how and what command should I be using? or if there
is a different way please do share.

2b) Also I am looking to monitor whether domain A is in the same plane as
domain B or if it has gone up or down in space with respect to domain B?
How can I monitor this feature?
I appreciate your help.

Thank you

James