<span style="font-family: courier new,monospace;">Hello,</span><br style="font-family: courier new,monospace;"><br style="font-family: courier new,monospace;"><span style="font-family: courier new,monospace;">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.</span><br style="font-family: courier new,monospace;">
<br style="font-family: courier new,monospace;"><span style="font-family: courier new,monospace;">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.</span><br style="font-family: courier new,monospace;">
<br style="font-family: courier new,monospace;"><span style="font-family: courier new,monospace;">I tried instead to define the z-distance of the waters relatively to the COM of the acyl chains (</span><span style="font-family: courier new,monospace;">my terminal acyl beads are named C4A and C4B, and the water residues PW</span><span style="font-family: courier new,monospace;">):</span><br style="font-family: courier new,monospace;">
<br style="font-family: courier new,monospace;"><span style="font-family: courier new,monospace;">centerbilayer = com of name "C4[AB]"</span><br style="font-family: courier new,monospace;"><span style="font-family: courier new,monospace;">resname PW and within 0.5 of centerbilayer<br>
<br>However, as expected, this defines a sphere around the COM, not a z-slab. Is there anyway to achieve that using g_select?<br><br>Another approach to count pore waters like:<br>resname PW and within 0.8 of name "C4[AB]"<br>
<br>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.<br><br><br>Any suggestions are welcome.<br>
<br>Manuel Melo<br></span>