Dear all,
I would like to simulate how positive ions interact with DNA polymer.
The structure is like some cylindrical shape attached to negatively charged particles
with the form of double Helix.
I put cylinderical rod by fix indent command, then
My question is about how to bind the negatively charge molecules.
In my simulation box, I have positively charged ions.
After negatively charged particles around the cylinder interacting with positive ions,
both negative and positive ions move.
I was thinking about using fix freeze to fix these negatively charged molecules
at the initial positions, but my atom_stlye is full type.
fix_freeze is a part of granular type package. So, I was unsuccesful for doing this.
My another thought is : if I increas the mass of the negatively particles much bigger than
the positive ions, the negatively charged particles moves very slowly....
However, I think that this is not a proper way to do it.
If you know how to bind these negatively charged molecules at a fixed
initial positions around cylinderical DNA rod,
please let me know.
Thank you for any comments from you.