[gmx-users] Re:A question about Periodic boundary condition
hailong at seas.ucla.edu
Tue Jul 20 22:23:43 CEST 2004
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.
>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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