[gmx-users] Protein going out of the box

nikhil damle pdnikhil at yahoo.co.in
Wed Jul 15 09:09:29 CEST 2009


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 ?


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