James Starlight wrote:
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 ?
You still have a dodecahedral box. The default representation is a simple
triclinic cell. A true compact representation can be obtained with:
trjconv -pbc mol -ur compact
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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