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 - 15:30:04 PST
