The protocols under Simulation serve the following types of users:

1. Novice protein modelers and computational chemists who are interested primarily in running pre-defined simulation protocols to provide simple minimization or dynamics of the molecular structure under study. Novice protein modelers and computational chemists will find that the protocols are an easy way to run predetermined workflows with a minimal amount of configuration.
2. Expert protein modelers and computational chemists who are interested in running several simulation steps independently and trying out different parameterizations.

Analysis Goals

You can use Simulation methods to:

• Analyze molecular trajectories
• Calculate energies using molecular mechanics or QM-MM based methods
• Calculate interaction energies
• Equilibrate a molecule with molecular dynamics
• Perform a dynamics simulation to adjust the temperature of a molecule
• Perform molecular dynamics on a pre-equilibrated molecule
• Minimize a molecule using molecular mechanics or QM-MM
• Calculate the radial distribution function for two sets of atoms in a trajectory
• Solvate a system by adding water molecules
• Perform a set of minimization and equilibration steps followed by molecular dynamics
• Calculate fundamental motions (Principal Components) of a trajectory
• Prepare structures for simulation using the forcefield tools
• Apply constraints on atoms in structures before performing simulation analysis
• Analyze molecular trajectories

Simulation Tasks

The following table describes the basic tasks that are possible with the Simulation methods. Read more..