md

This option controls the molecular dynamics (MD) simulation details.

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.

plumed_fn

Value	A file name
Default	None

If this is given, Qbics will apply enhanced sampling algorithms defined in the file in PLUMED library. For PLUMED input file grammar, please refer to its PLUMED manual.