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

Mark Abraham mark.j.abraham at gmail.com
Mon Jul 29 14:05:59 CEST 2013

There is lots of stuff. Please look in manual 7.4 and 8, which bring
order to the the morass of available tools.


On Mon, Jul 29, 2013 at 12:29 AM, jayant james <jayant.james at gmail.com> wrote:
> 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
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