Hi there,
The third script in the soak-type series allows you to soak a periodic structure. This can be useful if you have built and equilibrated complex structures and want to see the effect of adding solvent.
When you are solvating a structure in a 3D periodic cell, there can be large areas of occupied volume where solvation can not occur as there is already structure present. In order to save on close contact calculations, this script uses the field values from a Solvent Surface calculation to give an initial guess as to whether the molecules can be added. Once a guess passes the solvent surface test, a close contacts calculation is used as in other soak-like scripts.
This script currently requires the presence of a solvent surfaces, generated using the Atom Volumes and Surfaces tool, and a Field Probe. As you currently cannot create these in script, you must add these manually before running the script.
Hope you find it useful.
Best regards,
Stephen
The third script in the soak-type series allows you to soak a periodic structure. This can be useful if you have built and equilibrated complex structures and want to see the effect of adding solvent.
When you are solvating a structure in a 3D periodic cell, there can be large areas of occupied volume where solvation can not occur as there is already structure present. In order to save on close contact calculations, this script uses the field values from a Solvent Surface calculation to give an initial guess as to whether the molecules can be added. Once a guess passes the solvent surface test, a close contacts calculation is used as in other soak-like scripts.
This script currently requires the presence of a solvent surfaces, generated using the Atom Volumes and Surfaces tool, and a Field Probe. As you currently cannot create these in script, you must add these manually before running the script.
Hope you find it useful.
Best regards,
Stephen
