Hi Everybody,
Wish somebody help me to understand the following situation: Consider the MD simulation of two interacting molecule (first one on the left and the second one on the right) in a unit cell: The second molecule is interacting with the right side of the first one. Then, the second molecule start to get far from the first one and to get out of the unit cell, lets say the right-hand face of unit cell. Under the PBCs it has to enter from the the left-hand face and it interacts with the first molecule from the left side of the first molecule, while before getting out the cell it was interacting with the right side of the first molecule. I wonder if such simulation is correct...? I mean before getting out of cell the second one was interacting with the first one from its left side and if it interfaces the cell wall, it interact with the first molecule from its right side. There is a jump and I don't know how to deal with that during the simulation..
Before crossing the boundary, a particle is interacting with the other particle in the neighboring image cell. After crossing the boundary it interacts with the same particle in the unit cell. Probably it will be helpful for you to think about the PBC in terms of the unit and surrounding image cells simultaneously.
Hi Abdallah, thanks for the answer. I wonder if does this mean that one particle is interacting with two of others at the same time? If so then it isn't still the system I want throught which just one particle is interact with another one..
It depends on the range of the interaction and the size of the system. In case of long range electrostatic interactions, a particle will strongly interact with more particles within the unit cell and in the neighboring cells and it would be very expensive to compute these interaction directly. Thats why ewald sum methods are used.
Dear Zeynab
If you want to just simulate the interaction between those two particles *only*,
maybe you have to do it under Free Boundary Condition (FBC), instead of PBC.
Under FBC, when the second particle getting out of the cell,
it will just get out with out interacting further with the first particle anymore.
We use PBC to simulate a cell, surrounded by the cell itself simultaneously.
So whats happen in the cell, also happen in the surrounding cells, simultaneously.
Hi Joy, Thanks for your answer. As far as I know, doing molecular dynamics simulation we need to reduce the surface effects to catch the macroscopic properties. Moreover the molecules move around so much and I don't know exactly how I can do free boundary conditions.. Maybe by increasing the side length of the cell? That's expensive and increases the computation time I guess...
Hi Abdallah, then maybe increasing the size of the unit cell helps..?
Dear Zeynab
It is true, if we simulate a cell inside the bulk of materials, we have to reduce or even remove the effect of surface.
However, when you wrote "the second molecule start to get far from the first one and to get out of the unit cell", I thought that the molecule get off 'the surface' of your simulation cell.
So maybe you should elaborate more on, what is the true physical meaning of "get out of the unit cell"? Is it means that "the molecule get far and further away ...." or ...
I already mentioned that the PBC is on. Then by means of unit cell I meant the original unit cell which goes under the PBC. When molecule crosses the cell side then it enters in the periodic image of the unit cell. In the other way when the molecule get out of the unit cell from right side, then it enters in the periodic image located on the right side of original unit cell, starting to interact with the first molecule from the left side...
Yes. Thats exactly PBC.
So by your next question:
===
I wonder if such simulation is correct...?
===
It depends on what do you want to simulate.
If you are trying to simulate a cell inside a bulk materials, it should be 'correct'.
But if you want to simulate interaction of *only* two molecules,
and the 2nd should be go out the cell far far away, without further interaction with the first molecule, I think PBC is not applicable.
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