Module 3 : Molecular Dynamics Strategy

Lecture 17 : Non-Bonded Interactions

.

Thus we have:

Here Pd is the desired pressure and tp is the time constant for pressure fluctuations and . At each step the volume of the cell is scaled by a factor of  and the molecular centre of mass by a factor .Thus we have:

This method when combined with a method of temperature control  creates trajectories in the NPT ensemble. For the NPT ensemble Hoover (1985) gave the following equations for pressure control.

 

here  is given by Eq 49b. is the Boltzmann constant and f  is the frictional force. Here we have to specify the desired pressure Pd, time constant tp, decay time  and instantaneous temperature of the piston. In addition, the damping coefficients  and desired temperature of the molecule T are also specified for maintaining the constant temperature. For bulk solvent/fluid the instantaneous pressure of a simulation cell will have mean square fluctuations of  kT/ ()  where β is the isothermal compressibility, having root mean square (RMS) of 100 bar for 10,000 atom bimolecular system [Lifshitz and Landau,1985].