2 PLACING KCSA IN A MEMBRANE 30
image and the total number of atoms in your system: having a smaller
water box is a cheap way of making a smaller syste m.
Size of simulation cell. Periodic boundary conditions are generally
used to avoid surface effects and because its use p ermits the effi-
cient computation of long-range electrostatic interactions. However,
if the size of the simulation cell is too small, periodic images will
interact with themselves affecting the outcome of the simulation.
When choosing the size of your membrane patch and water box, be
sure to leave at least 15
˚
A of space between the protein and the
simulation cell boundaries on each direction. Heavily charged pro-
teins may require even more spacing. O ne can also use the Debye
length of the solution as a good criteria to determine the distance
b etween periodic images. In any case, take into account that the
example provided here i s designed for users with limited access to
computational resources (a larger membrane patch would be desir-
able).
2 We will make our system a nice cuboid, ∼ 2 × 38
˚
A on the plane of the
membrane. Type the following commands to do this:
package require solvate
solvate kcsa popc.psf kcsa popc.pdb -o kcsa popc water TEMP -b 1.5 \
-minmax {{-38 -38 -39} {39 39 50}}
The -b 1.5 option tells solvate to remove atoms within 1.5
˚
A of the
solute.
Now let’s take a look at what solvate has produced.
3 Delete the kcsa popc molecule and load, if not already loaded, the files
kcsa popc water TEMP.pdb and kcsa popc water TEMP.psf.
4 Show only segid WT1 to WT99. By default, the segid of the water pro-
duced by solvate begins with the prefix WT.
You can see that solvate put some water inside the lipid bilayer and around the
protein (Fig. 9). We don’t want this, so we must once again remove some atoms.
5 Type in the Tk Console window:
set all [atomselect top all]
$all set beta 0
set seltext "segid WT1 to WT99 and same residue as abs(z) < 25"
set sel [atomselect top $seltext]
$sel set beta 1
set badwater [atomselect top "name OH2 and beta > 0"]
set seglist [$badwater get segid]
set reslist [$badwater get resid]
(30 Seiten)
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