Can aspect ratio of the box affect the simulation results?

I am simulating hydrate formation using two different boxes but with the same number of molecules. The first box is a cube with equal edges. The second box is a cuboid that has one side unequal to the two other sides. The hydrate forms in the first box but not in the second box. Can it be because of the differences in the box shapes despite having the same type and number of atoms within the simulation box?

If this is an activated process (and it likely is), then there can be many factors that determine if something happens within a given time frame or not. So you need to do many series of simulations with different decorrelated starting conditions to see how well this can be reproduced. You also have to make certain, that you are not subject to any finite size effects which might artificially increase the activation barrier.

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