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

tenghl hailong at seas.ucla.edu
Tue Jul 20 22:23:43 CEST 2004

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,


>Hi Hailong,

>The best thing to do is to anticipate on the stretch when setting up the 
>box. That is, make the box large enough to also contain the stretched 
>conformation. When you use a rhombic dodecahedron box, you'll probably 
>get a very large volume, but since DNA is elongated you can probably do 
>with a rectangular, or preferrably a hexagonal prism, box. You have to 
>be sure to keep the DNA from rotating then, since that might still cause 
>images to see each other. I believe a method to constrain rotational 
>motions was available in Gromacs 3.2.1, otherwise I can provide a 
>version of 3.1.4 which has such constraints.

>Hope this helps,


>>tenghl wrote:

>>Dear all,
>>I'm simulating DNA-Stretch process. I use bond, angle, dihedral and pair potential for DNA molecule. But I'm confused how to apply periodic boundary condition since the length of DNA will change. Should I change box size by hand?
>>Best regards,
>>Hailong Teng

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