[gmx-users] Lyzosyme with ligand tutorial

James Starlight jmsstarlight at gmail.com
Mon Oct 24 18:26:54 CEST 2011

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

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 ?

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