[gmx-users] Rupture force definition

Rakesh Mishra rockinbhu at gmail.com
Fri Jan 19 06:52:07 CET 2018

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
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.


On Wed, Jan 17, 2018 at 6:20 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

> On 1/17/18 7:09 AM, Rakesh Mishra wrote:
>> Dear,
>> ​Justin​
>> I have one  query regarding pulling of si-rNA (having chain-a and
>> chain-b).
>> Here, I am pulling 3' end of chain-a and fixed 3' end of chain-b
>> (diagonally apposite ). I am doing pulling using gromacs with constant
>> velocity rate using Umbrella sampling. after finalization of pulling
>> before
>> umbrella sampling, we got two output file i.e.
>> 1- force/time (f= force)
>> 2- x/time     (x= pulling distance between two ends)
>> in first case of f/t, initially force increases and then after some  time,
>> force starts
>> to decrease (looks like gaussian curve, not exactly gaussian, because lot
>> of fluctuation). So my question is that, what this peak (of increasing and
>> decreasing curve ) represents. can I define this peak as a rupture force
>> or
>> breaking force of two strands of si-rna or something else.
> If you change the force constant, you'll get a different maximum force, so
> I wouldn't ascribe any real physical property to this number. The maximum
> force can inform you about the interactions that are perhaps most relevant
> to stability, but that's also a path-dependent behavior; if you pull in a
> different direction, you will probably get a different result.
> -Justin
> --
> ==================================================
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
> 303 Engel Hall
> 340 West Campus Dr.
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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*

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