Molecular Dynamics Simulation

Molecular Dynamics Simulation is an interface to minimization and molecular dynamics routines provided by MMTK, which is included with Chimera. Amber parameters are used for standard residues, and Amber's Antechamber module (also included with Chimera) is used to assign parameters to nonstandard residues.

Thanks to Victor Muñoz Robles and Jean-Didier Maréchal (The Computational Biotechnological Chemistry Team, Universitat Autònoma de Barcelona; funding from Ministerio de Ciencia e Innovación, Generalitat de Catalunya) for implementing this tool. See also: Minimize Structure, MD Movie, the Sophia plugin to Chimera

This tool was developed for teaching about molecular dynamics using simulations on small molecules. Compared to dedicated packages for molecular simulation (Amber, Gromacs, others), the calculations are relatively slow and parameter options few. Although it may be useful for limited sampling and relaxation of macromolecular structures and complexes, this tool is not suitable for long simulations on macromolecules, such as needed to predict changes in stability or binding energy. For such applications, other packages should be used instead.

There are several ways to start Molecular Dynamics Simulation, a tool in the MD/Ensemble Analysis category.

Select model: The model of interest should be chosen by clicking to highlight its name in the list of models. All of the atoms for simulation should be included in this model; any other models will be ignored.

The dialog has four tabbed sections, in order of typical use:

Only one section is shown at a time, and clicking the tab for another brings it to the front.

Prep Structure

Structure preparation is the same as for Minimize Structure and consists mainly of running Dock Prep to perform several tasks to prepare the system for energy calculations. These tasks may include calling AddH to add hydrogens and Add Charge to associate atoms with partial charges and other force field parameters. One of the following should be chosen before Dock Prep is started:

See the Minimize Structure documentation for details on force field parameters and associated limitations.


Buttons are provided to add solvent and counterions, if desired, by running the Solvate and Add Ions tools, respectively.

Periodic Boundary Conditions should only be used when a solvent box has been added. In that case, the “rgn size” reported by Solvate in the Reply Log can be entered as the dimensions of the (orthorhombic) periodic box. Alternatively, checking the Automatic box size option will use the bounding box of the chosen model along X, Y, and Z plus 2 Å padding on all sides. The automatic box size will be reported as the “universe size” in the Reply Log when the calculations are run.

Constraints Etc.

ForceField Options

** If periodic boundary conditions are used, no distance cutoff d should exceed half of the smallest box dimension. **

Electrostatic interaction method: Lennard-Jones interaction method:

Run Parameters

Settings are shown separately for the four subsections:

** Regardless of which subsection is shown, clicking Run will initiate running all stages of the calculation (sequentially), so care should be taken to set the desired parameters in all subsections beforehand. **




Other Runtime Options

After the completion of any MD run, the (cumulative) trajectory will be opened automatically in the MD Movie tool for playback, recording, and/or various analyses.
UCSF Computer Graphics Laboratory / May 2020