Adjusting the Volume for a Repulsive Harmonic System

Repulsive harmonic (RH) systems will nearly always have a volume that is different from the desired one when they are built. A tool has been provided, scale_simulation_box.py, to adjust the system volume by scaling the box size and site coordinates uniformly. This scaling should be done after the atoms are mapped to particles and the coarse-grained system is generated.

In RH models, the density of the coarse-grained sites (particles) is chosen based in part on how many atoms are mapped onto these sites. This density corresponds to an average volume per coarse-grained site, which can then be used to estimate the appropriate volume and thus the dimensions that the RH system should have. Given an average site volume, X, the command to use is:

$SCHRODINGER/run scale_simulation_box.py -p X disordered-system.mae scaled_system.mae

The file scaled-system.mae can be read into Maestro and used as the coarse-grained system.