[gmx-users] Rupture force definition
jalemkul at vt.edu
Wed Jan 17 13:50:59 CET 2018
On 1/17/18 7:09 AM, Rakesh Mishra wrote:
> 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
Justin A. Lemkul, Ph.D.
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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