[gmx-users] Strange problem.complex out of Box after EM

Justin A. Lemkul jalemkul at vt.edu
Thu Nov 17 18:54:54 CET 2011

Please change the subject line to the relevant topic and do not paste the entire 
digest.  I guess the archive is already somewhat hopeless, but let's not make it 
worse :)

Saba Ferdous wrote:
> Dear Justin,
> I have set 1.5 dodecahedron. i centered the complex in box.
> complex.gro, complexsol.gro and complex_sol_ions.gro seems inside in 
> box. I m using VMD for visualization. i have rotated it in 3D
> while when after EM step, i visualize em.gro then half complex seems 
> outside the box. is there any way to center em.gro after energy 
> minimization?

Again, this is just a matter of visualization.  There is nothing wrong and 
nothing needed to fix.  You can rewrap the periodic cell with

trjconv -pbc mol -ur compact

if you find you want more convenient visualization.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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