molecular dynamics

Molecular dynamics (MD) simulations propagate the system in time by numerically integrating Newton's equations of motion, which makes it possible to sample configurations at a given temperature, equilibrate structures and generate trajectories for later analysis. EasyHybrid provides access to the three MD integrators available in pDynamo: Velocity Verlet, Leap Frog and Langevin. They can be used with MM, QC or hybrid QC/MM potentials.

Molecular dynamics simulations can also be performed by accessing:

Main Menu > Simulate > Molecular Dynamics

An overview of the Molecular Dynamics window can be seen in Figure 1. In EasyHybrid, the reference system is determined by the active radiobutton in the treeview of the main window (note that each system is associated with a reference color).

General parameters

• Initial Coordinates: the set of coordinates used as the starting point of the simulation. The combobox only displays objects associated with the selected system (if the object has more than one frame, the last one is used).

• Integrator: the integration algorithm: Velocity Verlet Dynamics, Leap Frog Dynamics or Langevin Dynamics. The parameters shown in the window change according to the chosen integrator (see below).

• Number of Steps: the total number of integration steps (default: 1000). The simulated time is the number of steps multiplied by the time step.

• Temperature – Start (K): the simulation temperature, in kelvin (default: 300 K). Initial velocities are assigned according to this temperature.

• Time Step (ps): the integration time step in picoseconds (default: 0.001 ps = 1 fs).

• Log Frequency: how often (in steps) energies and other information are written to the log (default: 10).

• Random Seed: the seed of the random number generator used to assign initial velocities and, for Langevin dynamics, the random forces (default: 44561). Using the same seed with the same input reproduces the same simulation.

Velocity Verlet Dynamics

Velocity Verlet integrates the equations of motion at constant energy (NVE). The temperature can be controlled by velocity rescaling:

• Temperature: the scaling option: constant (velocities are rescaled to keep the start temperature), linear or exponential (the temperature changes from the start value to the stop value along the simulation, which is useful for heating or annealing protocols).

• Stop (K): the final temperature (default: 400 K). Only available when the scaling option is linear or exponential.

• Temp. Scale Frequency: how often (in steps) velocities are rescaled (default: 100).

Leap Frog Dynamics

The Leap Frog integrator allows simulations with temperature coupling and, optionally, pressure coupling (NPT ensemble). When it is selected, the following fields are shown:

• Temp. Coupling: the coupling constant of the thermostat (default: 0.1).

• Pressure Coupling (checkbox): turns pressure control on or off.

• Pressure: the target pressure (default: 1.0 atm).

• Pressure coupling constant: the coupling constant of the barostat (default: 2000.0).

Pressure control only makes sense for periodic systems, for example a solvated protein in a box.

Langevin Dynamics

Langevin dynamics adds friction and random forces to the equations of motion, so the system behaves as if it were coupled to a heat bath at the chosen temperature. When it is selected, the following field is shown:

• Collision Frequency: the friction (collision) frequency, in ps-1 (default: 25). Larger values couple the system more strongly to the heat bath.

Saving the trajectory

The Save Trajectory checkbox controls whether frames are written to disk. The entry next to it sets the name of the trajectory:

• Working Folder: the folder where the trajectory is saved.

• Format: the trajectory format (pDynamo / pkl, saved as a .ptGeo folder).

• Trajectory Frequency: how often (in steps) a frame is saved (default: 10).

Click Run to start the simulation. When it finishes, the trajectory can be loaded as a new object of the system, played with the Trajectory Handler and analyzed with the tools of the Analysis menu (RMSD, distances, alignment, etc.).