The build_geometry Stage

System Preparation
  • Overview
  • Default Configuration

The System Builder panel uses this stage to build a Desmond model system, such as adding solvent, ions, or a membrane bilayer. The build_geometry stage is usually followed by an assign_forcefield stage to complete the preparation of a Desmond model system. The keywords specific to this stage are given in Table 1.

Table 1. Keywords for the build_geometry stage

Keyword

Description

add_counterion

Add counterions to the system. With add_counterion.type, you can select the type of the counterion. The option add_counterion.number controls how many counterions are added. Allowed values can be a number or the value neutralize_system which adds as many counterions as needed to neutralize the overall charge of the system.

box

Specify box.shape to select the appropriate shape of the simulation box. Allowed values are cubic, orthorhombic, or triclinic. Set box.size to the appropriate dimension of the simulation box, for example box.size = [10.0 10.0 10.0]. If box.size_type = absolute, the dimension refers to the absolute size of the simulation box. If box.size_type = buffer, the dimensions refer to the minimum distance between box edge and solute. For membrane protein systems, only box.shape = orthorhombic and box.size_type = buffer are allowed.

ion_awaydistance

Minimum distance between the added ions and the atoms specified by ion_awayfrom. Valid values are non-negative real numbers. Default: 10.0.

ion_awayfrom

Do not place ions near the specified atoms. Valid value is a list of atom indices. Default: [].

membrane_box

Add a membrane box to the system. Specify the type of lipid with membrane_box.lipid. Allowed values are DOPC, DPPC, POPC, or POPE. Specify the size of the membrane box with membrane_box.size which should be a list of three values.

override_forcefield

Determine the force field for the system. This does not assign the force field, but is used to place the solvent, ions, and membrane around the solute. Valid values are OPLS_2005, OPLS4 and OPLS5.

rebuild_cms

Extract the component CTs from a full system CT. All other settings are ignored. Valid values are true, false, or a block like:

{ membrane = ASL-expression | ""
 solvent = ASL-expression | "" }

If the value is not false, the component CTs are extracted from the full system CT. The block value allows you to you can specify which atoms belong to the membrane component CT and which belong to the solvent component CT. Default: false.

rezero_system

Reset the origin of the coordinates to the center of mass of the solutes. Allowed values are true, false. Default: true.

salt

Add additional salt to the simulation box. The type of positive ions can be specified with salt.positive_ions. Allowed values are Li, Na, K, Mg2, Ca2, Zn2, Fe2, Fe3. The negative ions can be specified with salt.negative_ions. Allowed values are F, Cl, Br, I. The salt concentration can be specified with salt.concentration (in units of M).

solvent

Solvent type. Allowed values are WATER, SPC, TIP3P, TIP4P, TIP4PEW, TIP4PD, TIP5P, METHANOL, OCTANOL, DMSO. Values are case sensitive. WATER is a synonym for SPC. Default: SPC.

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

{
   add_alchemical_ions = false
   add_counterion = {
      ion = Na
      number = 0
      where = []
   }
   box = {
      shape = orthorhombic
      size = [10.0 10.0 10.0 ]
      size_type = buffer
   }
   box_shape = cubic
   buffer_width = 10.0
   compress = "$MAINJOBNAME_$STAGENO-out.tgz"
   csb_file = ""
   dir = "$[$JOBPREFIX/$]$[$PREFIX/$]$MAINJOBNAME_$STAGENO"
   distil_solute = true
   dryrun = false
   effect_if = {list}
   ion_awaydistance = 10.0
   ion_awayfrom = []
   jlaunch_opt = []
   jobname = "$MAINJOBNAME_$STAGENO"
   membrane_box = {
      lipid = POPC
      size = [10.0 10.0 10.0 ]
   }
   minimize_volume = false
   neutralize_system = true
   only_merge_ct = []
   override_forcefield = OPLS_2005
   prefix = ""
   preserve_box = false
   preserve_ffio = true
   rebuild_cms = false
   remove_overlapped_crystal_water = false
   remove_overlapped_solvent = true
   rezero_system = true
   salt = {
      concentration = 0.15
      negative_ion = Cl
      positive_ion = Na
   }
   scale_solvent_vdw = 1.0
   should_skip = false
   should_sync = true
   solvate_system = true
   solvent = water
   solvent_file = {str}
   struct_output = ""
   title = {str}
   transfer_asap = false
}