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
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