Justin, hello!<br><br><br>I have forced with some problem during final stage of your turorial.<br><br>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).<br>
<br>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 )<br>
<br>I've tried examined why this might occur but have not found possible explanations.<br><br>I've examined box coordinates of the all .gro structurs obtained after each of the stages and all of them contained such box vectors<br>
<font face="Arial"><font size="3">7.85059 7.85059 5.55120 0.00000 0.00000 0.00000 0.00000 3.92529 3.92529<br><br>As I understood It's correspond to the system in the </font></font>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 ? <br>
<br><br>James<br>