Re: [AMBER] Axis of a helix as a collective variable

From: Akshay Prabhakant <>
Date: Thu, 20 Dec 2018 23:00:14 +0530

I need a solution without the use of plumed patching for ambermd.

On Thu, Dec 20, 2018 at 10:43 PM Akshay Prabhakant <> wrote:

> I have a collection of atoms which forms a helical structure. I need to
> find the vector corresponding to the axis of this helix, since I will be
> using that as a collective variable in an umbrella sampling simulation. Can
> someone please suggest me a way around?
> A follow up question: How can i get angle between two vectors in amber as
> a collective variable?
> Thanks in advance.
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Received on Thu Dec 20 2018 - 10:00:03 PST
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