[gmx-users] Using g_select to detect water pores in a bilayer

Manuel Nuno Melo m.n.melo at rug.nl
Thu Jan 27 15:18:46 CET 2011


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

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

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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