[gmx-users] the problem of the periodic boundary

[Justin A. Lemkul]

kecy_wu at sina.com wrote:
> Hello, I use the 2D periodic boundary along the x and y axises, it has a 
> strange thing. my solvent is dodecane,  I view the output  trajectory in 
> the VMD, for one molecule, it has some part in
> 
> the left(top), and some in the right(bottom), it still connections to 
> each other, how to solve this problem?
> 

Sounds to me like the normal outcome of PBC:

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

-Justin

>  
> 
> Thank you !
> 

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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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