[gmx-users] Rupture force definition

Rakesh Mishra rockinbhu at gmail.com
Wed Jan 17 13:09:31 CET 2018


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.

* 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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