Justin, hello!
I have forced with some problem during final stage of your turorial. I dont know why but after NPT phase my sytem has occured in the standart cubic box instead of dodecahedron (after all previosly phases my system was in correct box). So when I've passed my system in the MD stage- it's moved back into normal dodecahedron box but on the placement where previously system was. So as the consequence I've obtained protein in the wrong place ( some of its parts were outside new box ) I've tried examined why this might occur but have not found possible explanations. I've examined box coordinates of the all .gro structurs obtained after each of the stages and all of them contained such box vectors 7.85059 7.85059 5.55120 0.00000 0.00000 0.00000 0.00000 3.92529 3.92529 As I understood It's correspond to the system in the dodecahedron box but my ntp.gro structure with the same is in the cubic box ( with the above box coordinates as well). Why its might occured and were else information of the box coordinates is present exept of initial structure gro file ? James
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