Thank you Justin! I understand usually for regular equilibration, restraints should be enough. But I am still wondering to what extent position restraint can restrain my atoms. In fact, I ran a relatively longer NVT using position restraints and I saw that both the absolute coordinates of my "restrained" atoms and the distances between my "restrained" atoms changed by ~0.01nm and I think that is not negligible any more. I don't know whether this is normal or a problem that I should somehow fix. Any thoughts? Thank you!
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