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

From: Osman, Roman <roman.osman.mssm.edu>
Date: Thu, 20 Dec 2018 18:54:03 +0000

Try this:

On Dec 20, 2018, at 1:37 PM, Wesley Michael Botello-Smith <wmsmith.uci.edu<mailto:wmsmith.uci.edu>> wrote:

If you are using this as a means to set up the angle between the axes of a
pair of helices as a collective variable, one potential option would be to
pick groups at the ends of each vector to serve as centers of mass in a
COM_TORSION (dihedral) collective variable. This would work moderately well
for helices that remain relatively rigid. It would capture parallel
scissoring motion between the axes of the two helices.
If, on the other hand, the two helices are extending out from a common
point then you could capture a true 'angle' collective variable by defining
that point as an appropriate center of mass and then defining appropriate
centers of mass for the ends of the two helices for use in a 'COM_ANGLE'
collective variable.

-Dr. Wesley Botello-Smith

On Thu, Dec 20, 2018 at 9:33 AM Akshay Prabhakant <
akshayresearch16.gmail.com<mailto:akshayresearch16.gmail.com>> wrote:

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

On Thu, Dec 20, 2018 at 10:43 PM Akshay Prabhakant <
akshayresearch16.gmail.com<mailto:akshayresearch16.gmail.com>> 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?

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Roman Osman
Department of Structural and Chemical Biology
Mount Sinai School of Medicine
New York, NY 10029
Tel: 212-659-8627
Fax: 212-849-2456
e-mail: roman.osman.mssm.edu<mailto:roman.osman.mssm.edu>

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Received on Thu Dec 20 2018 - 11:00:03 PST
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