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2 PLACING KCSA IN A MEMBRANE 29

Figure 8: Top and side views of KcsA embedded in a membrane patch (ob-

tained using ﬁles kcsa popc.psf and kcsa popc.pdb). Note the lack of overlap

between the protein and the membrane.

2.4 Solvation and Ionization

We will now solvate and ionize the system. VMD’s Solvate plugin is quite

simple: it places your solute in a box of water of a speciﬁed size, then removes

water which is within a certain cut-oﬀ distance. We will remove any water which

adds inside the lipid bilayer as well. Steps 2-6 are also included in the script

solv remove.tcl.

1 First, let’s use the minmax option of the measure command to see how big

our water layer is:

mol delete all

mol new kcsa popc.psf

mol addfile kcsa popc.pdb

set water [atomselect top water]

measure minmax $water

You should get something like the following:

{-37.5699996948 -37.6370010376 -39.4020004272} \

{38.3590011597 38.8470001221 49.1450004578}

The size of the water box we make should be of similar size in the xy-

plane. In fact, a water box slightly smaller in the xy-plane is desirable,

since non-equilibrated membranes tend to shrink. In the z-direction, there

is more choice. The size is often dictated by the distance to the p eriodic

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SanDisk Membrain Software Manual do Utilizador Página 29