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

[Mark Abraham]

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

Mark

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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