md

type

Value	NVE Microcanonical ensemble, constant number of particles, volume, and energy
	NVT Canonical ensemble, constant number of particles, volume, and temperature
	fep-NVE Free energy perturbation calculation for microcanonical ensemble
	fep-NVT Free energy perturbation calculation for canonical ensemble
Default	NVE

Define the MD simulation type.

dt

Value	A real number
Default	0.0005

The time step in ps. For systems not containing hydrogen atoms, dt can be set to 0.001 ps.

num_steps

Value	An integer
Default	10

The number of MD steps to be run.

output_freq

Value	An integer
Default	1

The number of steps that MD information is output. The trajectory, velocity, and gradient will be output to disk.

temp

Value	A real number
Default	273.15

Define the initial temperature for NVE simulation, and the targeted temperature for NVT simulation.

temp_nhc_length

Value	An integer
Default	5

The length of Nose-Hoover chain to control the temperature. Usually an integer larger than 2 is enough.

temp_nhc_tau

Value	A real number
Default	0.5

The time-constant of Nose-Hoover chain to control the temperature in ps.

vel_fn

Value	A file name
Default	None

If this is given, the initial velocities will be set from this XYZ file (in Angstrom/ps). Otherwise, velocities will be generated from Boltzmann distribution. For example:

md   
  vel_fn mol-vel.xyz
end

Initial velocities will be read from mol-vel.xyz.

max_dr

Value	A real number
Default	5

The maximum allowed atomic displacement per step in Angstrom. If an atom mover more than max_dr in a step, Qbics will stop the MD simulation since the system may crash due to the too fast motion.