[gmx-users] protein near the edges of simulation box

Shima Arasteh shima_arasteh2001 at yahoo.com
Thu Jun 14 09:47:29 CEST 2012

Dear gmx friends,

I put a protein in a simulation box filled of water molecules and entered the mdrun command. After the simulation, I found the protein near one of the edges of the box and not in center. What is the problem? Anyone may suggest me?

Does it mean that the simulation is meaningless? 

I expect the protein to stay in the center of box and goes unfold by passing the time.

Thanks in advance

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