When attempting to build an amorphous cell of a rigid polymer, it’s quite often difficult to get the amorphous cell successfully built. One alternative is to use the “Ramp Density” option, by building the cell at a (much-) lower density first, and subsequently ramp the density to the desired value. Unfortunately, there can be cases where even the “Ramp Density” procedure fails to produce the desired density. Is there an alternative in such cases to still arrive at the desired density from the much lower initial density?
An effective solution can be isostatic pressing through an MD run in NPT. Be sure to use the Anderson barostat where the shape of the cell is preserved while the volume (and hence the density) can vary. Save the frames periodically. Play back the trajectory, and pick the frame that has the desired density.
The attached example is a polystyrene amorphous cell built to a density of ca. 0.72 g/cm^3, that comes with an MS installation, by default under,
C:\\Program Files (x86)\\BIOVIA\\Materials Studio
Polystyrene has a density between 0.96–1.04 g/cm^3. Using the procedure described above, by applying an isostatic pressure of 0.1 GPA, one can arrive at a density of ca. 0.97 g/cm^3, as in the final frame in the attached trajectory.
