Gromacs PBC: What the difference when I put periodic-molecules "yes" or "no" with pbc in all xyz direction?

04 April 2018 0 5K Report

I checked it in the manual which says if periodic-molecules is set to no, "molecules are finite, fast molecular PBC can be used" and if it is set to yes " for systems with molecules that couple to themselves through the periodic boundary conditions, this requires a slower PBC algorithm and molecules are not made whole in the output ".

Can anyone please explain what does this mean and when we can set it to yes or no?

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