[gmx-users] Re:A question about Periodic boundary condition

Tsjerk Wassenaar t.a.wassenaar at chem.rug.nl
Wed Jul 21 10:19:14 CEST 2004

Hi Hailong,

I hadn't caught that you wanted to have it infinite, but in that case 
you have to allow the box to adapt to the conformation of the DNA, that 
is, you have to use pressure coupling. In setting up the box, you still 
have to anticipate on the amount of stretch, since in the stretched 
conformation the surrounding layer of solvent will be thinner than in 
the contracted conformation. In the stretched configuration you still 
want to have about 2 nm between periodic images, to keep them from 
direct interaction and to allow normal diffusion of solvent. Then 
recalculate the dimensions of the box from that volume to match the 
initial length.
Since an infinite molecule can't rotate around it's shorter axes, you 
can use a hexagonal prism and don't have to worry about rotational 

Hope it helps,


tenghl wrote:

>Hi Tsjerk,
>Thank you for your kind reply. My purpose is to simulate an infinite long DNA molecule, that's why I want to use PBC. 
>If I make the box large enough to contain the stretched conformation, I'm afraid that my system may not be able to
>represent an infinite long DNA molecule.
>Best regards,

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