Production MD를 시작하기 전에 시스템을 목표 온도와 압력 조건에 안정적으로 적응시키는 과정입니다. 처음부터 모든 조건을 한 번에 적용하면 단백질이나 주변 환경이 급격히 변할 수 있습니다. 따라서 초기에는 단백질의 위치를 일정하게 유지하도록 position restraint를 적용하고, 평형화가 진행함에 따라 restraint의 세기를 단계적으로 낮춥니다. 이를 통해 시스템이 목표 온도와 압력 환경에 서서히 적응하면서 안정화되도록 합니다.
CANDDIE는 시스템이 안정적으로 평형에 도달할 수 있도록 단계별 Equilibration 최적화된 설정 값을 제공합니다. 그대로 사용하시는 것을 권장합니다. (단, 베타 테스트 기간에는 예외적으로 간소화된 버전으로 제공됩니다.)
Production을 시작할 때 각 원자에는 설정된 온도에 해당하는 초기 속도(initial velocity)가 무작위로 부여됩니다. 이때 사용되는 난수 시드(random seed)를 replica마다 다르게 설정하기 때문에, 동일한 구조와 simulation 조건에서도 각 replica는 서로 다른 궤적(trajectory)을 생성합니다. 하나의 궤적만으로는 특정 결과가 우연히 나타난 것인지 판단하기 어려우므로, 여러 replica를 수행하여 결과의 평균과 replica간 편차를 함께 확인합니다.
Report에서 세 replica가 유사한 경향을 보이면 재현성 있는 결과로 해석할 수 있습니다. 반대로 replica간 차이가 크다면 시스템의 sampling이 충분하지 않을 가능성이 있으므로, 더 긴 simulation 또는 추가 replica가 필요한지 검토할 수 있습니다.
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