[gmx-users] Pulling doubt

[Rakesh Mishra]

Hi all

This pulling protocol of gromacs is still in doubt

Please tell me if there is  dsDNA of chain A (12 bp)
and  complimentary strand B(12 bp)  like

chain A-   3' - 5'
chain B-   5' - 3'
If I pull  5' end  of strand  A and made 5' of B as a reference group
along the helical direction under constant velocity pulling. And both the
chains are free ( no restraint) ,
under this situation will the 5' of chain B (act as reference group) feel
the equal and opposite force like 5' end of chain A where pulling is
applied .
Due to this equal and opposite force both the strand will move opposite to
each other or not .


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*With Best-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, +918777496532*