[gmx-users] Rupture force definition

Justin Lemkul jalemkul at vt.edu
Fri Jan 19 13:52:50 CET 2018

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 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


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