Molecular Dynamics with HyperChem

HyperChem provides versatile tools for exploring the structure, stability and properties of molecules using molecular mechanics and quantum mechanics. It offers simple ways to produce 3D molecular structures on screen, a choice of four molecular mechanics force fields and nine semi-empirical quantum mechanical methods, and a selection of geometry optimization techniques to search for stable structures. The graphical user interface links all of HyperChem's extensive visualization and computational capabilities, giving you the ability to run molecular dynamics calculations using either molecular mechanics or quantum mechanics methods to calculate the interatomic forces.

Molecular Dynamics Applications

Molecular Dynamics calculations simulate the behavior of molecules at specified temperatures or energies and can be used in many applications, including:

Investigating conformational flexibility.
Using simulated annealing (high-temperature dynamics followed by slow cooling) to search for low-energy minima.
Using dynamics with restraining forces to build experimental data into your simulations.
Illustrating reaction mechanisms with dynamics trajectories using potential surfaces determined by semi-empirical quantum mechanical calculations.

Versatility in Molecular Dynamics Calculations

HyperChem offers a range of options for setting up molecular dynamics calculations, including the ability to:

Carry out molecular dynamics calculations using any of HyperChem's molecular mechanics force fields or SCF quantum mechanical methods.
Run the calculations at constant energy, or keep the system close to a constant temperature.
Specify the length and temperature of the heating, run and cooling phases of a dynamics run.
Specify the temperature step to be used for heating and cooling phases.
Carry out molecular mechanics simulations subject to restraining forces and/or with portions of the system fixed in space.
Control the rate of collection, averaging, and display of data during a run.
Save the end point of the run, including velocities, so that you can resume where you left off.
Carry out calculations on isolated molecules or on systems solvated in a periodic box of water molecules.
Plot selected energetic and structural quantities while running or playing back a simulation.
Assign specific initial atomic velocities, or let HyperChem choose velocities according to a Maxwell-Boltzmann distribution with a user-specified random number seed.

HyperChem uses the leap-frog integration algorithm for molecular dynamics calculations.

Analysis Capabilities

HyperChem also provides powerful facilities for analyzing the results of your dynamics calculations, including the ability to:

Save the run in a "snapshot" file for later replay and analysis.
Statistically average energetic quantities such as the total, potential, and kinetic energies and temperature.
Statistically average structural quantities such as distances (bonded and non-bonded), angles and torsion angles, as calculations are carried out.
Graph energetic or structural quantities.
Control sampling range and frequency for averaging and graphing.
Control the display while the calculation or replay is in progress, so you can rotate, translate or zoom your view of the system as it moves.

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