[gmx-users] Protein out of box

[Alif M Latif]

Dear GROMACS users and developers,
 
I'm having problem with my protein structure after md simulation. The protein structure was outside of the simulation box after the simulation. My configuration include my protein structure, DMSO and water. After equilibration simulation the protein was still in the simulation box. However, after 2 ns of production simulation, only the protein structure was out of the simulation box. DMSO and water were still in the box. 
My question is, is this a sign of something that I did wrong (i believe so), or I can just ignore it and try centering the protein again in the box. Can anyone please help me out? Comments and suggestions are greatly appreciated.
Thank You,
 Muhammad Alif Mohammad Latif 


Department of Chemistry
Faculty of Science
Universiti Putra Malaysia
43400 UPM Serdang, Selangor
MALAYSIA 


      
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