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

Saba Ferdous saba.bsbi154 at iiu.edu.pk
Thu Nov 17 11:10:00 CET 2011

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..

Many thanks with anticipation


Saba Ferdous
Research Scholar (M. Phil)
National Center for Bioinformatics
Quaid-e-Azam University, Islamabad
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