Desmond Tutorial

1 Desmond Tutorial
Introducing Desmond
Desmond is an advanced classical molecular dynamics simulation system, which has an
intuitive graphical user interface integrated in the Maestro molecular modeling environment.
Using Desmond, you can perform in silico simulations of small molecules, proteins,
nucleic acids, and membrane systems to study the interactions of complex molecular
assemblies. With Desmond, you can generate high‐quality simulation trajectories of long
time scales as well as compute a variety of thermodynamic quantities. Desmond trajectories
can be visualized and analyzed using numerous tools in Maestro and VMD.
This tutorial assumes a basic knowledge of molecular mechanics and molecular dynamics.
For those users who have not yet used Maestro for molecular modeling, an overview
of the Maestro environment is included.
Beyond basic molecular modeling, there are a number of steps that must be performed on
a structure to make it viable for simulation with Desmond. Each of these steps mandates
an understanding of certain concepts and differing approaches that can be taken.
To enable novices and advanced users alike to process the information in this tutorial, the
organization of the tutorial includes:
• A step‐by‐step example that describes, at a high level, how to perform a simulation on
a simple protein.
• In‐depth concept sections that cover the detailed information users will need in order
to perform a simulation similar to our example.
This tutorial also includes conceptual information and steps for performing free energy
perturbation (FEP) calculations. FEP is useful for performing “alchemical” ligand mutations
to determine binding free energy differences, which is a crucial task for such applications
as computational drug design.
September 2008 D. E. Shaw Research 1