[gmx-users] separation of two strands of DNA during of simulation

[Justin A. Lemkul]

shahab shariati wrote:
> Hi gromacs users
>  
> I runing md simulation of DNA for 20 ns (5000 frame). I see trajectory 
> during simulation. I see in some times, two strands of DNA are seprated. 
> simulation now is in frame of 4600. is this state true and rational? 

Not likely.  This sounds like a normal consequence of periodic boundary conditions:

http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions

-Justin

>  
> any help will highly appreciated! 
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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