Simulation

Simulation

The protocols and tools under Simulation allow you to run energy calculations, solvation, energy minimization, and molecular dynamics simulations using the CHARMm and other programs.

The protocols under Simulation serve the following types of users:

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.
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. The table includes links to topics found in Help that discuss relevant tasks.

For a discussion of the following tasks	See the following topic(s)
Analyze trajectories of a molecular system.	Analyze Trajectory tools
Apply a forcefield to a molecule so it can be used by simulation protocols.	Forcefield tools
Set up constraints on molecules that control how they behave under simulation conditions (distance restraints for example).	Constraints tools
Analyze a loaded molecular dynamics trajectory.	How to run the Analyze Trajectory protocol
Evaluate the energy of a specified structure.	How to run the Calculate Energy protocol
Calculate the nonbonded interactions (i.e., the van der Waals term and the electrostatic term) between two sets of atoms in a specified structure or trajectory.	How to run the Calculate Interaction Energy protocol
Given an ensemble of configurations from a trajectory, compute the radial distribution function (pair correlation) for two specified sets of atoms.	How to run the Radial Distribution Function protocol
Solvate a molecule in water (explicit solvation).	How to run the Solvation protocol
Launch a simulation cascade of the following standard steps: minimization 1 + minimization 2 + heating + equilibration + production.	How to run the Standard Dynamics Cascade protocol
Given a trajectory, calculate the principal components of the molecular system based on quasiharmonic analysis.	How to run the Trajectory Principal Component Analysis protocol
Create a simulated molecule that includes trajectory information saved as conformations, each annotated with various standard properties calculated by CHARMm.	How to run the Standard Dynamics Cascade protocol How to run the Dynamics (Equilibration) protocol How to run the Dynamics (Heating or Cooling) protocol How to run the Dynamics (Production) protocol
Launch CHARMm simulation protocols consisting of individual steps (for example production), potentially using the output of previous steps.	How to run the Minimization protocol How to run the Dynamics (Equilibration) protocol How to run the Dynamics (Heating or Cooling) protocol How to run the Dynamics (Production) protocol
Examine intermediate files generated during a simulation protocol.	Simulation Intermediate Files

Nonbond cutoffs

Cutoff distances for nonbonded interaction shown as defaults in the Simulations protocols should be consistent with forcefield parameterization as shown in the following table.

Forcefield	Cutoffs
Charmm 19:	6.5, 7.5, 8.0
CHARMM:	11, 14, 15
Charmm 22:	10, 12, 13
Charmm 27:	10, 12, 14
CFF	8, 9, 9.5

Temperature controls

Temperature controls for dynamics protocols are handled as follows:

For both heating and equilibration, simple velocity re-assignment at the desired temperature(s) is used to maintain thermal equilibration.
In the Dynamics (Production) protocol, and for the production stage in the Standard Dynamics Cascade protocol, Berendsen's weak coupling scheme (Berendsen, et al. 1984) is used to achieve constant temperature dynamics in the NVT ensemble, while the Hoover's extended system constant pressure and temperature algorithm is used for simulation in the NPT ensemble.

Working with multiple molecules

When there are multiple molecules in a system, the simulation protocols only take one molecule as the Input Typed Molecule parameter.

To run a multiple molecule simulation on a complex system, drag and drop the molecules into a single molecule in the Hierarchy View, and run the simulation on this combined molecule.

Running parallel Simulation protocols

Running Simulation protocols in parallel is supported on a multi-processor server. To do this, you will need to set the advanced parameter Number of Processors to a number that is a power of 2. Refer to the Troubleshooting Help topic for further information.

Further information

Forcefield Tools Panel
Constraints Tools Panel
How to save intermediate files
Theory - Simulation