Berendsen manostat – Computational Chemistry

Berendsen manostat – Computational Chemistry: This time we will discuss one of the ensembles in molecular dynamics simulations that NPT ensemble, where N (number of molecules), P (pressure) and the temperature is kept. The previous article we have discussed how to maintain a constant temperature by using a Berendsen thermostat.

So, before entering how to maintain constant pressure, the first question how do we measure the pressure in the simulation? er wrong, ding before that if we do not maintain the pressure or temperature of the ensemble that we use is NVE, where E or chemical potential will be kept, if the temperature is kept so ensemble NVT and if the temperature is maintained tetep the NPT ensemble * N and V I assume tetep in the third ensemble.

Okay, back to the question how to measure the pressure in the simulation? the answer is by using the ideal gas equation. where we have a relationship pV = HCV. from here the ideal gas equation we add the virial equation. What is that? Imagine if two particles interact, eh btw, how do we know that two particles interact with each other? yap, we could measure of the potential energy due to the long distances the potential energy can be said to be close to 0 so that no interaction occurs. Besides? we can tell from the style. where we know that the value of w = F x delta_r_ij or w = - F x delta_v_ij. nah ΣΣ virial equation is then ditambahken to the ideal gas equation that had been mentioned.

if the NVT ensemble we perform scaling of the speed (Berendsen thermostat) then the NPT ensemble we do sacaling to the length of the box simulations using lambda coefficient. where lambda (Berendsen manostat) can be written as follows:

Berendsen-manostat

So now we detailed the case in the NPT ensemble. first, if we have a cube box with all the same length, the lambda ribs can be applied to all sides, this is simple, the case is known as isotropic (where all three in the same direction) in kassus semi-anisotropic and anisotropic the lambda value must be calculated differently for each axis x, y and z.

anisotropic

So, we would never know the term transition phase, when in college first material only vaguely pack and bu lecturer explained that somehow I do not understand. well when we do the NPT ensemble then chances are we can experience a transition phase, it can you know if the matrix transpose ent F, T. then you would get in a diagonal matrix FxVx FyVy FzVz. hence the term semi-anisotropic because there form the diagonal matrix.

All right, enough so first and hopefully!

# To prevent the phase transition we should really use the rigorous scaling of the temperature and the time step so that the molecule will not move much.