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

From: Pratul Agarwal <>
Date: Thu, 20 Dec 2018 20:23:53 +0000

You will have to define your own collective variable based on what you are trying to accomplish. The other messages in thread gave you some good pointers about helix axis definition and using center of mass of atoms to define the angle between two helices.

Practically speaking, you will have to use "nmropt" keyword if you want to define angle between center-of-mass of groups of atoms and apply restraints for umbrella sampling.

Pratul K. Agarwal, Ph.D.
(Editorial Board Member: PLoS ONE, Microbial Cell Factories)

On 12/20/2018 12:13 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 - 12:30:03 PST
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