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 ?
Regards,
Nikhil
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