The PressureCtrl command sets the pressure control mode.

Conformational changes of the simulated biomolecules lead to fluctuations in density. If the simulation box has a constant size, changes in density lead to changes in pressure. This is somewhat unrealistic, because proteins normally fold and function in a constant pressure environment.

If PressureCtrl is activated, YASARA uses the time averaged solvent density as a probe for the pressure in the box. The box is then rescaled to arrive at the target solvent density and thus pressure. Simulations are normally run at a pressure of 1 atm and 298 K, where the experimentally determined water density is 0.997 g/ml. The densities of other solvents are listed at the end.

Instructions on how to fill the cell with a certain solvent are provided at the FillCellWater and FillCellObj commands.

Since the solvent density depends on the temperature, it has to be adjusted for simulations run at temperatures other than 298K. As an example, the water density as a function of temperature is listed below:

Rescaling does not only involve the simulation cell, but includes also the atom coordinates. An exception are simulations in non-periodic cells with atoms outside the cell. In this case, only the cell is rescaled. Note that pressure control in non-periodic cells is of limited use : if the cell size increases, the surface tension causes the water molecules to detach from the cell wall and form a liquid droplet, that is not influenced by pressure control and cell scaling.

The Axis parameter defines along which axes the cell is rescaled to reach the requested water density. It is sometimes helpful to keep the length of certain cell axes fixed, for example when simulating objects like membranes that wrap around the periodic boundaries. Note however that the solvent density is not a reliable pressure indicator when there are no solvent molecules left in a certain plane through the cell.

Densities of various solvents at 298K in g/ml:

PressureCtrl Off

Disable pressure control.

PressureCtrl SolventProbe,Name=HOH,Density=0.997

Measure water density and slowly resize simulation cell to reach 0.997 g/ml.

PressureCtrl SolventProbe,Name=DMS,Density=1.096,Axis=Y

Measure density of the dimethyl sulfoxide solvent and resize cell along the Y axis to reach the density 1.096 g/ml.