Desmond Tutorial

Desmond Tutorial
Finishing Preparations for Desmond Simulation
Figure 5.2 Advanced Options for simulation jobs
Parameters for nonbonded
interactions.
Thermostat and
barostat parameters.
Controls output files
for simulations.
Parameters for
setting harmonic
restraints.
Other parameters
such as those
defining atom
groups.
Multiple time step
parameters and
constraints.
The Advanced Options window has several tabs:
• Ensemble—Contains thermostat and barostat parameters.
• Interaction—Contains parameters for computing non‐bonded interactions.
• Restraint—Provides a table in which multiple sets of atoms can be subjected to harmonic
restraint with a user‐defined force constant. Atom selection can be directly
input as an ASL expression or you can click the Select button to bring up the Atom
Selection dialog box.
• Output—Includes the names of various Desmond output files, and allows you to
specify how often these files are updated during the simulation. For example, different
energy terms are recorded in the energy sequence file in user‐defined intervals.
Snapshots of the simulation are periodically saved in the trajectory file and the
entire simulation state is also saved at user‐defined intervals in a checkpoint file.
Desmond simulations can be restarted from checkpoint files with bitwise accuracy.
• Misc—Provides control over miscellaneous parameters, including the definition of
atom groups. Currently, two different atom groups are recognized by Desmond. A
`frozenʹ atom group means a set of atoms that move during the entire MD simulation
as a rigid body. (NOTE: in Desmond, unfrozen atoms cannot be connected to
frozen atoms). For example, an entire protein molecule can be frozen (during equilibration),
but one cannot freeze only the heavy atoms, or just certain residues. In that
case, restraints should be used. Also note that frozen atoms cannot be used with
NPT simulations, because the Virial will be incorrect. The other atom group termed
cm_moi is used to define parts of the system whose center of mass motion is set to
zero. In most protein simulations the protein center of mass motion is set to zero to
prevent the protein from translating and rotating in the simulation box. Atom
62 D. E. Shaw Research September 2008