The solvate_slab_builder Stage

Overview
Default Configuration

This stage adds solvent to the slab in the system, using the disordered system builder. This builds a cube of the specified solvent molecules, with each replicated molecule being randomly rotated in 3 dimensions. The slab must be along the z-axis for this stage to successfully run.

See disordered_system_builder_driver.py Command Help for more information.

The stage requires the user to specify a file with the relevant molecules. The default stage configuration is as follows:

solvate_slab_builder {
	molecules = 100 
	density = .25
	scale_vdw = .8
	seed = 645
	interface_vacuum_buffer = 10
	interface_buffer = 5
	molecules_file = ""
}

Table 1. Keywords for the solvate_slab_builder stage
Keyword	Description
`molecules`	The number of molecules to place in the system cell.
`density`	The initial density target for building the cell.
`scale_vdw`	Scaling factor for VDW radii to use when computing clashes.
`seed`	Random seed to use.
`interface_vacuum_buffer`	The number of angstroms to expand the periodic boundary condition beyond the components to create a vacuum buffer between the slab and mirror image of the scaffold (for interface scaffolds).
`interface_buffer`	The buffer in angstroms between scaffold and disordered system (for interface scaffolds).
`molecules_file`	Solvent molecule to replicate around the slab.

Default configurations for the solvate_slab_builder stage. A {type} value is shown for keywords which do not have defaults set. See General multisim Stage Keywords for descriptions of general keywords

{
   compress = "$MAINJOBNAME_$STAGENO-out.tgz"
   density = 0.25
   dir = "$[$JOBPREFIX/$]$[$PREFIX/$]$MAINJOBNAME_$STAGENO"
   dryrun = false
   effect_if = {list}
   interface_buffer = 5
   interface_vacuum_buffer = 10.0
   jlaunch_opt = []
   jobname = "$MAINJOBNAME_$STAGENO"
   molecules = 100
   molecules_file = ""
   prefix = ""
   scale_vdw = 0.8
   seed = 645
   should_skip = false
   should_sync = true
   struct_output = ""
   title = {str}
   transfer_asap = false
}