Constant Energy, Temperature, or Pressure

Molecular dynamics simulations can produce trajectories (a time series of structural snapshots) which correspond to different statistical ensembles. In the simplest case, when the number of particles N (atoms in the system), the volume V, 

By applying Eq. (45), the velocities v are scaled by the factor A to come closer to the desired temperature Tq i is defined in Eq. (45). 

T(f) corresponds to the actual temperature at the time t, At is the integration time step, and the relaxation time represents the strength of the coupling (smaller values mean stronger coupling to the bafli). If the coupling is too strong (r smaller 

However, it is common practice to sample an isothermal isobaric ensemble NPT, constant pressure and constant temperature), which normally reflects standard laboratory conditions well. Similarly to temperature control, the system is coupled to an external bath with the desired target pressure Pq. By rescaling the dimensions of the periodic box and the atomic coordinates by the factor // at each integration step At according to Eq. (46), the volume of the box and the forces of the solvent molecules acting on the box walls are adjusted. 

Also in this case, Tp corresponds to a relaxation time which determines the coupling of the modulated variable to the external bath. The pressure scaling can be applied isotropically, whidi means that the factor is the same in all three spatial directions. More realistic is an anisotropic pressure scaling, because the box dimensions also change independently during the course of the simulation. 

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