Hi, I used bilayer that consisted of 128 DOPC lipids as DOPC128.pdb as the primary bilayer and insert protein in bilayer with Inflategro program. when i expanded the bilayer, two DOPC molecules exited from box. i simulated this system and obtained the thickness of bilayer with GrigMAT_MD. i want to subtract the thickness of pure bilayer from the bilayer that contain the protein.
would one please elaborate step by step how to subtract the thickness of the pure bilayer( 128 DOPC) from the bilayer (126 DOPC) that contains the protein to get two-dimensional maps of ∆Z that indicate deviation from the thickness of pure bilayer ? Thanks in advance, Afsaneh
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