[gmx-users] A question about Periodic boundary condition

Tsjerk Wassenaar t.a.wassenaar at chem.rug.nl
Tue Jul 20 10:53:40 CEST 2004

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
>gmx-users mailing list
>gmx-users at gromacs.org
>Please don't post (un)subscribe requests to the list. Use the 
>www interface or send it to gmx-users-request at gromacs.org.

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