[gmx-users] A question about Periodic boundary condition
t.a.wassenaar at chem.rug.nl
Tue Jul 20 10:53:40 CEST 2004
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,
>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?
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