[gmx-users] Rupture force definition

[Justin Lemkul]

On 1/19/18 12:52 AM, Rakesh Mishra wrote:
> Dear Justin
>
> Thanks for your explanation . Yes I am agree that it will depend on the k
> value and path direction.
> Let suppose we map the experimental spring constant and rate then it will
> be some how relevant for my study.
>
> My another query is the same from umbrella sampling of puling code.
> If I restrain some different molecule (let C ) and give the reference
> molecule (let B) and pulling molecule (Let A), then
> I found that , when I pull molecule A in + x direction then C has
> immobility while  molecule B is feeling opposite force w. r.  t.  molecule
> A. i. e. if  molecule A is moving
>   along + x direction then reference molecule B starts to move in - x
> direction.
> Now I want to know that in pulling code, does reference molecule and
> pulling molecule connected with imaginary spring, due  to this newton third
> law is applying here.

Yes, of course. The biasing potential is applied to both species 
specified in the group setup; we use a convention of "pulled" and 
"reference" group for defining a suitable reaction coordinate, but the 
forces are always applied to any group involved in this process.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==================================================