Qbox List

Hello,

Many thanks for your answers, Francois.
I'd like to ask about the thermostat of AIMD.
It seems that an example AIMD file is for NVE simulation, not NVT simulation. Is it right?

If so, would you let me know what thermostat method and its paramters should be recommended for AIMD of liquid water?
What initial veolicity assignment method and/or keyword would be used generally for the AIMD of qbox in the case that initial velocities are missing?
After the equilibration at certain temperature (NVT), NVE simulation, rather than NVT simulation, would be preferred for analysis (avoiding possible artificial effects?)?

Best regards,

Young

Hello Young,

To run an NVT simulation, you can first initialize velocities using the randomize_v command, for examplewhich will initialize atomic velocities using a Maxwell-Boltzmann distribution of temperature 330 K. Then you can use a thermostat in the simulation using e.g. This will use the Bussi-Donadio-Parrinello thermostat that is the preferred choice. See the document of the thermostat variable http://qboxcode.org/doc/html/usage/vari ... thermostat for details. The BDP thermostat has been shown to have very little effect on dynamical properties, so it can be used during the production runs after equilibration (see the BDP papers).

It is also good practice to include the following commands before the run command: The rseed command sets a random seed for the random number generator using by the thermostat. This ensure that multiple simulations do not use the exact same sequence of random numbers. The reset_vcm command resets the velocity of the center of mass to zero. This prevents a global drift of the system that may result from small numerical errors in the forces.

Best,
Francois