Actually I am planning on finding the rotation of the axis of helix w.r.t.
to its initial state, since in my reaction, the axis of the helix
rotates(and also the helix itself) as we go from the reactant to the
product, so please can you suggest me something along these lines?
On Fri, Dec 21, 2018, 4:49 AM Pratul Agarwal <pratul.agarwal-lab.org> wrote:
> This actually helps me! I didn't know about the NFE module, I am still
> catching up on new features of AMBER18. Thank you Dr. Botello-Smith, I will
> definitely look into it.
>
> Pratul K. Agarwal, Ph.D.
> (Editorial Board Member: PLoS ONE, Microbial Cell Factories)
> Web: http://www.agarwal-lab.org/
>
>
>
>
> On 12/20/2018 6:11 PM, Wesley Michael Botello-Smith wrote:
>
> As a clarification, nmropt was pretty much the only option for AMBER17 and
> below (as Dr. Agarwal mentioned in a previous post).
> As of AMBER18, you can now use the NFE module instead. See chapter 21.6.2
> of the AMBER18 manual for details on how to use the NFE module for this, or
> check out chapter 26 for details on doing this under the previous nmropt
> method.
> Hope this helps!
>
> -Dr. Wesley Botello-Smith
>
> On Thu, Dec 20, 2018 at 12:26 PM Pratul Agarwal <pratul.agarwal-lab.org
> ><mailto:pratul.agarwal-lab.org>
> wrote:
>
>
>
> 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)
> Web: http://www.agarwal-lab.org/
>
>
>
>
> 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 - 19:30:03 PST
