The assign_forcefield Stage

System Preparation
Structure Modification
  • Overview
  • Default Configuration

This stage can be used to assign the force field to a model system. You can either keep or replace existing assignments. The keywords are given in Table 1.

Table 1. Keywords for the assign_forcefield stage

Keyword

Description

forcefield

Specify the force field to use. Valid values are: OPLS_2005, OPLS4, and OPLS5. Default: OPLS_2005.

hydrogen_mass_repartition

Redistribute the mass of heavy atoms to bonded hydrogen atoms to slow-down high frequency motions. Valid values are true, false. Default: false.

restraints

Specify internal coordinate restraints on bonds, angles, and torsions for specified atoms. Restraints can be a critical part of a simulation; see Simulation Restraints for more information on this keyword.

Restraints set in this stage using the restraints.new keyword are “permanent”—they are inherited by all subsequent stages. Permanent restraints can be overridden in a particular stage, but will still be applied in subsequent stages.

water

Specify the water model to use. Valid values are: SPC, SPCE, TIP3P, TIP3P_CHARMM, TIP4P, TIP4PD, TIP4PEW, TIP4P2005, TIP5P, none. Values are case sensitive. Default: SPC

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

{
   assign_is_infinite = false
   atom_group = retain
   compress = "$MAINJOBNAME_$STAGENO-out.tgz"
   core_hopping_fepio = true
   dir = "$[$JOBPREFIX/$]$[$PREFIX/$]$MAINJOBNAME_$STAGENO"
   dryrun = false
   effect_if = {list}
   fail_on_lewis_failure = true
   fep_enhance_sampling_dihedral = false
   fep_retain_angle = true
   fepio_mode = 2
   forcefield = OPLS_2005
   humble = false
   hydrogen_mass_repartition = false
   jlaunch_opt = []
   jobname = "$MAINJOBNAME_$STAGENO"
   macromolecule_conf_restraint = {
      backbone = {
         alpha = 1.0
         fc = 50.0
         name = harm
         schedule = ""
         sigma = 10.0
      }
      calpha_rung = {
         alpha = 1.0
         fc = 5.0
         name = harm
         schedule = ""
      }
      dihedral_schedule = ""
      enable = false
      sidechain = {
         alpha = 1.0
         fc = 50.0
         name = harm
         schedule = ""
         sigma = 10.0
      }
   }
   make_alchemical_water = true
   pose_conf_restraint = {
      alpha = 1.0
      dihedral_schedule = ""
      enable = false
      fc = 50.0
      max_ring_size = 999
      name = harm
      schedule = pose_dihedral_restraint
      sigma = 10.0
   }
   prefix = ""
   print_restraint = false
   restrain = none
   restraints = {
      existing = ignore
      new = []
   }
   should_skip = false
   should_sync = true
   struct_output = ""
   title = {str}
   transfer_asap = false
   use_zob_property = true
   water = SPC
}