Equilibration에서는 position restraint를 단계적으로 완화하면서 시스템이 안정화됩니다. 각 단계에서는 restraint의 세기가 일정하기 때문에 RMSD가 비교적 안정적으로 유지되지만, 다음 단계로 넘어가 restraint가 약해지면 원자들이 움직일 수 있는 범위가 넓어지면서 RMSD가 새로운 수준으로 증가할 수 있습니다. 이러한 “상승 → 안정화 → 상승 → 안정화” 과정이 반복되면서 RMSD 그래프가 계단 형태로 나타날 수 있습니다. 일반적으로 restraint가 점차 약해지는 후반 단계에서는 구조의 움직임이 더 자유로워지므로 RMSD 변화 폭도 커질 수 있습니다.
RMSD가 각 단계 전환에 따라 계단 형태로 증가한 후 다시 안정화되는 양상은 restraint가 설정된 순서에 따라 완화되고 있음을 보여줍니다. 따라서 이러한 패턴 자체는 이상 현상이 아니라, Equilibration이 의도된 과정에 따라 진행되고 있음을 나타내는 정상적인 양상으로 볼 수 있습니다.
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