Desmond Tutorial

Preparing a Desmond simulation with the System Builder
System Builder Output File Format
NOTE
• Apply a buffer distance to each dimension of the simulation box. A typical buffer distance
is 10 Å, which is equal to the usual real space Coulombic interaction cutoff for
long‐range electrostatic calculations.
• Set the absolute size and shape of the box.
Next, by clicking the Minimize Volume button you can instruct the System Builder to minimize
the box volume by aligning the principal axes of the solute with the xyz or diagonal
vectors of the simulation box—essentially, you can align the protein structure so that it fits
inside its simulation box more comfortably. However, this method is only recommended
if the solute is not allowed to rotate during MD simulation.
Selecting the Show boundary box option displays a helpful, translucent graphical representation
of the simulation box in the Workspace.
System Builder puts the center of gravity of the solute at the center of the simulation box.
As a consequence, fairly non‐spherical proteins will appear to shift toward one side of the
box, leaving only a thin water buffer on that side. This may not be ideal from a visual perspective,
but in terms of periodic boundary conditions, this is perfectly adequate. It is not
the distance between the outer surface of the protein and the near face of the simulation
box that matters; rather, it is the sum of two such distances with respect to the opposite
sides of the protein that is important.
System Builder Output File Format
The System Builder writes the simulation system in a composite model system file with
the extension .cms. .cms files are essentially multi‐structure Maestro files that are suitable
for initiating Desmond simulations. Typically, the total solvated system is decomposed
into five separate sections in the .cms file: protein (solute), counter ions, positive salt ions,
negative salt ions, and water molecules. The System Builder also writes the force field
parameters in the .cms file. You can find detailed documentation of the .cms file format in
the Desmond User Guide and the Schrödinger Desmond User Manual listed in “Documentation
Resources” on page 97.
Adding Ions
Click the Ions tab in the System Builder window as shown in Figure 4.3 to add ions to your
system. By default the System Builder automatically neutralizes the solute. For example, if
the solute has a net charge of +N, System Builder will randomly select N residues on the
surface of the protein with a positive formal charge and, respectively, place a negative
counterion in the vicinity of the selected residue. For negatively charged solutes, positive
counterions will be similarly positioned. The Advanced ion placement button allows you to
place counterions in a more sophisticated manner, but this procedure is illustrated in “Setting
Up Membrane Systems” on page 47 where membrane setup is discussed using a concrete
example.
• An arbitrary number of counterions can be added; for example, if there is a reason not
to neutralize the system (refer to the special note in “Setting Up Membrane Systems”
on page 47). Conversely, you may choose not to place any counterions.
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