[gmx-users] Protein going out of the box

[Mark Abraham]

nikhil damle wrote:
> Hello,
> 
> When I am running energy minimisation of protein-peptide complex, 
> minimised structure shows a space for the protein in water box; but 
> peptide remains inside the box while protein is seen outside.
> 
> Same occurs when I keep pbc = xyz and/or nstcomm = 1
> 
> in ..top file, I am including individual posre.itp files (posre_A.itp 
> and posre_B.itp) separately.
> 
> How should I fix this problem ?

See this page, in particular the bottom. 
http://oldwiki.gromacs.org/index.php/Periodic_Boundary_Conditions

Mark