Starting configuration for molecular dynamics

User discussions
1

I have to build a bilayer using a structure obtained in a previous MD simulation. In the structure, some chains of the molecules cross the simulation box as shown below. I added water layers to the structure as below. Since some of the structure parts are oriented out of the box, I would like to know whether doing the MD simulation for the prepared structure (below image) is correct or do I have to arrange the molecules in a manner that molecules are not going out of the box. Appreciate your help since I am new to MD.

Thank you.

image

2

Hi, I think you should ask yourself whether the molecules sticking out from the box overlap with the periodic image of other molecules. If not, it should be fine.
You can start a simulation with atoms outside the periodic box, as long as it doesn’t cause the system to explode.

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3

Thanks a lot for your clarification.