[gmx-users] Rupture force definition

[Rakesh Mishra]

Ok, thanks for learifivcation.
Dear Justin I have one  another query regarding
pulling using umbrella sampling. See these two lines below.

Eg.    Pull group   natoms    pbc atom  distance at start    reference at
t=0
                     1        31       1387
                     2        31       686                7.424 nm
7.424 nm

When we use grompp for obtaining .tpr file before mdrun of pulling. We see
2 lines which are shown just above .

My query is that why it is written 7.424 nm in the second line below the
distance at start (written in the first line).
I am asking because, in my thinking my object( reference group ) is very
close to wall ( nearly 2 nm away from the wall of yz. here I am
pulling in + x direction), which I can see in VMD.  Does this distance is
distance from the pull group to the reference group or
distance between pulled group to the wall near the reference group.






On Fri, Jan 19, 2018 at 6:22 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
>
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-- 
* Rakesh Kumar Mishra*
*  (RA)CSD  SINP Kolkata, India*

*E-mail - rakesh.mishra at saha.ac.in <rakesh.mishra at saha.ac.in> *

*Phone n. +91 9473662491, +91877749632*