Setting up a molecular dynamics calculation
In most cases a dynamics calculation is preceded by structure minimization. It may also be desirable to perform minimizations after the calculation on several of the conformations that were generated.
CASTEP dynamics calculations can be only performed for systems with P1 symmetry.
Defining the time step
A key parameter in the integration algorithms is the integration time step. A common rule-of-thumb used to pick the time step is that the highest frequency vibration should be sampled between 15 and 20 times in one cycle. For example, if the highest frequency is 20 THz, a typical optical mode frequency in an insulator, a time step of 2.5-3.3 fs is appropriate (period = 1/frequency = 50 fs). In water, the stretch frequencies are around 110 THz, indicating that a time step of 0.45-0.6 fs is required. You will probably be able to use a time step that samples the motion as few as 10 times in a cycle. However, you must check your choice of time step by monitoring energy conservation in the NVE ensemble. A thermostat in the NVT ensemble can completely mask inadequate integration.
The Time step can be increased to about 4-5 fs when the extended Lagrangian formulation (Steneteg 2010, Niklasson, 2011) is used.
To choose a time step
- Choose Modules | CASTEP | Calculation from the Materials Studio menu bar.
- Select the Setup tab.
- Click the More... button to open the Dynamics dialog.
- Select the Dynamics tab.
- Set the Time step in the text box.
Along with the related value Number of steps, Time step also determines the Total simulation time. Changes to the Dynamics time also affect the Number of steps.
Choosing an ensemble
You can control temperature of a CASTEP dynamics calculation, in order to simulate a system that exchanges heat with the environment. Under these conditions, the total energy of the system is no longer conserved and extended forms of molecular dynamics are required.
You can simulate several thermodynamics ensembles with a constant number of particles.
|
Ensemble |
Conditions |
Description |
|---|---|---|
|
NVE |
Constant-volume/constant-energy dynamics |
The Newtonian equations of motion, which conserve the total energy, are used. The unit cell is fixed. The temperature is allowed to vary. Energy is the constant of motion - it can fluctuate slightly, but there should be no systematic drift. |
|
NVT |
Constant-volume/constant-temperature dynamics |
The unit cell is fixed. A thermostat maintains a constant temperature. The dynamics are modified to allow the system to exchange heat with the environment at a controlled temperature. Several methods of scaling or controlling the temperature are available. |
|
NPH |
Constant-pressure/constant enthalpy dynamics |
The size of the unit cell is allowed to vary with a barostat to maintain constant pressure. The enthalpy is a constant of the motion. The size of the unit cell is allowed to vary, while the temperature is also allowed to vary. The enthalpy, which is a constant of the motion, is not allowed to vary beyond a set value between dynamics steps. |
|
NPT |
Constant-pressure/constant-temperature dynamics |
The size of the unit cell is allowed to vary with a barostat to maintain constant pressure. A thermostat maintains a constant temperature. Similar to NPH, except that temperature is controlled. Several methods of scaling or controlling the temperature are available. |
To choose an ensemble
- Choose Modules | CASTEP | Calculation from the Materials Studio menu bar.
- Select the Setup tab.
- Click the More... button to open the Dynamics dialog.
- Select the Dynamics tab.
- Select the required ensemble from the Ensemble list.
- Select the Options tab to enter parameters for the selected ensemble.
Constraints
Molecular dynamics in CASTEP obeys constraints on atomic positions and/or interatomic distances (bonds) imposed through the Materials Visualizer.
You can set such constraints using the Edit Constraints dialog, accessible from the
Modify menu.
To fix atomic positions in CASTEP you must check the Fix fractional position checkbox on the Atom tab
of the Edit Constraints dialog.