我在MD的时候设的iwrap=1，发现跑的过程中蛋白有部分跑出了溶剂盒子，请问这对结果分析有影响吗？如何才能使结构回归到盒子中心呢？

顶一个   

有人遇到这种情况吗？

Do you mean part of the protein denatured or it still holds the original structure but is just sticking out of the boundary. If it's the first case, there is definitely something funny about the structure. If it is the second case, you can do the following:
1. solvent the protein in the bigger water box (make sure you have at least 9-A water layer at any point wrapping about the protein
2. If the protein is not quite spherical, you might thinking of using irregular shape of water box and make sure everything is fully solvated and none of the protein atoms can see their image.

我的也出现这个问题，用center 或者image familiar恢复不了，实在太郁闷了