Hello, I have a coarse-grain lipid bilayer system with a pore-forming peptide. I am trying to use g_select to automate the detection of the opening of a water pore.
My idea is to count the number of water molecules within a certain z distance of the bilayer center, and flag a pore above a certain threshold. The problem is that the position of this z-slab cannot be hardcoded because my simulations are relatively long and there is sometimes a drift of the bilayer. I tried instead to define the z-distance of the waters relatively to the COM of the acyl chains (my terminal acyl beads are named C4A and C4B, and the water residues PW): centerbilayer = com of name "C4[AB]" resname PW and within 0.5 of centerbilayer However, as expected, this defines a sphere around the COM, not a z-slab. Is there anyway to achieve that using g_select? Another approach to count pore waters like: resname PW and within 0.8 of name "C4[AB]" also fails because the pore is lined by peptide molecules and a relatively large distance for the PW-C4 distance must be allowed. This means that interfacial waters will be frequently counted in. Any suggestions are welcome. Manuel Melo
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