Running Molecular Dynamics

Molecular dynamics with AMMP.

AMMP uses a stiffly stable predict and correct algorithm for molecular dynamics. Nose constraints are used to implement constant temperature, constant energy and constant PT dynamics.

V_maxwell initializes the velocities with a random Maxwell-Boltzmann distribution. (i.e. V_maxwell 300; for 300K).

V_rescale rescales the velocities. (i.e. v_rescale 290; to rescale to 290K).

Pac nstep dtime; Predict and correct dynamics. Nstep is the number of steps, Dtime = .00001 for 1 fs steps.

Pacpac nstep dtime; Iterated predict and correct dynamics. Somewhat more numerically accurate than pac.

Tpac nstep dtime T; Constrain the temperature to T (in kelvin).

Hpac nstep dtime H; Constrain the total energy to H. This is an example of a way to fake good dynamics.

Ptpac nstep dtime T P; Constrain the temperature to T, the pressure to P. Pressure is in kilopascal (101.325 kPa = 1atm). The volumes are not fully calibrated in this command. It is also necessary to slowly approach the desired conditions because this uses Andersens demon for volume constraints. Andersens demon is not fully stable and the system can explode.

Verlet nstep dtime; The verlet or leapfrog algorithm. Use at your own risk. This is here for historical reasons, and is occasionally useful.