[gmx-users] Rupture force definition

[Justin Lemkul]

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

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

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