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Steered Molecular Dynamics
In this section you will learn how to use Steered Molecular
Dynamics (SMD). In particular, you will explore elastic properties
and unfolding pathways while becoming accustomed to constant velocity
and constant force SMD simulations performed by NAMD.
- The basic idea behind any SMD simulation is to apply an external force
to one or more atoms, which we refer to as SMD atoms. In addition, you can keep another group of atoms fixed and study the behaviour of your protein under various conditions.
- In the following simulations, you will fix one atom of ubiquitin and pull on another one and, thereby, stretch and unfold ubiquitin.
Before running the actual simulations, you
will prepare your system and create the files needed.