Desmond Tutorial

Desmond Tutorial
Preparing a Desmond simulation with the System Builder
NOTE
NOTE
button to position the entry according to the saved transformation matrix. This way, all
proteins will be placed in the membrane in exactly the same position and orientation.
8. Finally, click the green Start button to start the membrane system setup. For 1su4, the
setup procedure should take 6–8 minutes. The resulting simulation system is shown
in Figure 4.14 on page 55. For better visualization, the protein is shown as a CPK
model and the lipid bilayer is highlighted in green.
The visible gap at the top and bottom of the lipid layer is the gap between the water
layer that is part of the DPPC model and the extra water layer, which was added to the
system to satisfy the boundary conditions. This is expected since the system is put
together from two different, pre‐equilibrated boxes of a solvated lipid bilayer and plain
solvent, respectively. The gap should go away after a relatively short equilibration
period. However, membrane systems should be equilibrated for an extended period of
time (up to a few hundred ns) to resolve the large hole that was carved out of the lipid
bilayer to accommodate the transmembrane part of the protein. The hole is shown for
the 1su4 structure in Figure 4.15.
The protein in the simulation box in Figure 4.14 is positioned so that the head of the protein
seems to protrude into vacuum. This is the result of a visual artifact discussed in
“Defining the Simulation Box” on page 44. System Builder puts the center of gravity of
the solute at the center of the simulation box. As a consequence, fairly non‐spherical systems
will appear to shift toward one side of the simulation box. Membrane systems are
extreme cases resulting in the view on Figure 4.14. This may not be ideal from a visual
perspective, but in terms of periodic boundary conditions, this is perfectly adequate. It is
a periodic image of the protruding part of the protein at the bottom of the simulation
box where there is plenty of water, that is used in the computation (see Figure 4.14).
54 D. E. Shaw Research September 2008