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

Justin A. Lemkul jalemkul at vt.edu
Thu Nov 17 12:51:43 CET 2011

Saba Ferdous wrote:
> Dear Gromacs users
> I am trying to simulate a protein complex. That complex has been 
> obtained after protein-protein docking.
> I have geneated topology, defined box and solvate, added ions 
> successfully. My complex is centered in box.
> but when I performed Energy minimization then my protein complex comes 
> out of box from one side.
> can any body help me in fixing this problem so that i could proceed 
> towards equilibrium steps..

There is no problem.  It is odd that EM would cause periodicity issues, but 
suggests that your protein is not centered properly or that your box is not 
large enough to accommodate it.  There may be some inconvenience for 
visualization (which can be fixed), but there is no such thing as "outside" in a 
periodic system.




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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