[gmx-users] Protein going out of the box

Mark Abraham Mark.Abraham at anu.edu.au
Wed Jul 15 09:14:24 CEST 2009

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. 


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