The concatenate Stage

Overview
Default Configuration

Several simulate stages can be concatenated in a single concatenate stage. This enables launching multiple simulate stages as a single process. This can be useful to accelerate workflows that consist of many short simulate stages. A concatenate stage produces a single set of output files.

The syntax for the concatenate stage looks like this:

concatenate {
  simulate = [
    { keywords }
    { keywords }
  ]
}

All keywords that can be used in a simulate stage can also be used inside the concatenate stage. Restraints defined with the restraints keyword must be defined in the first simulate block and can only differ in the force constant of the restraint. For example, it is not possible to start the concatenate stage with restraints = none and apply a restraint in a following simulate block. It is also not possible to change the type of restraint in a concatenate stage. Using the GCMC protocol inside a concatenate stage is not supported.

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

{
   annealing = false
   atom_group = none
   backend = {
   }
   bigger_rclone = false
   box = {}
   cfg_file = ""
   checkpt = {
      first = 0.0
      interval = 240.06
      name = "$JOBNAME.cpt"
      write_last_step = true
   }
   compress = "$MAINJOBNAME_$STAGENO-out.tgz"
   coulomb_method = useries
   cpu = 1
   cutoff_radius = 9.0
   dipole_moment = false
   dir = "$[$JOBPREFIX/$]$[$PREFIX/$]$MAINJOBNAME_$STAGENO$[_lambda$LAMBDA$]"
   dryrun = false
   ebias_force = false
   effect_if = {list}
   elapsed_time = 0.0
   energy_group = false
   eneseq = {
      first = 0.0
      interval = 1.2
      name = "$JOBNAME$[_replica$REPLICA$].ene"
   }
   ensemble = NPT
   fep = {
      i_window = {int}
      lambda = "default:12"
      output = {
         first = 0.0
         interval = 1.2
         name = "$JOBNAME$[_replica$REPLICA$].dE"
      }
      trajectory = {
         record_windows = [0 -1 ]
      }
      type = small_molecule
   }
   gaussian_force = false
   gcmc = {
      ene_name = "$JOBNAME$[_replica$REPLICA$]_gcmc.ene"
      first = 0.0
      gcmc_region = {
         cell_size = 0.22
         exclusion_radius = 2.2
         global_switching = {
            frequency = 0.2
            move_factor = 3.0
            spacing_factor = 2.0
         }
         region_buffer = 4.0
         track_voids = true
      }
      interval = 4.8
      ligand_file = {str}
      moves = {
         moves_per_cycle = 5000
      }
      mu_excess = -6.18
      seed = random
      solvent = {
         s_file = ""
      }
      solvent_density = 0.03262
      verbose = 0
   }
   glue = solute
   host = "$SUBHOST"
   jin_file = []
   jin_must_transfer_file = []
   jlaunch_opt = ["" ]
   jobname = "$MAINJOBNAME_$STAGENO$[_lambda$LAMBDA$]"
   jout = ""
   lambda_dynamics = false
   maeff_output = {
      center_atoms = solute
      first = 0.0
      interval = 120.0
      name = "$JOBNAME$[_replica$REPLICA$]-out.cms"
      periodicfix = true
      trjdir = "$JOBNAME$[_replica$REPLICA$]_trj"
   }
   meta = false
   meta_file = {str}
   msd = false
   prefix = ""
   pressure = 1.01325
   pressure_tensor = false
   print_expected_memory = false
   print_restraint = false
   randomize_velocity = {
      first = 0.0
      interval = inf
      seed = 2007
      temperature = "@*.temperature"
   }
   restrain = none
   restraints = {
      existing = ignore
      new = []
   }
   rnemd = false
   should_skip = false
   should_sync = true
   simbox = {
      first = 0.0
      interval = 1.2
      name = "$JOBNAME$[_replica$REPLICA$]_simbox.dat"
   }
   simulate = []
   spatial_temperature = false
   struct_output = ""
   surface_tension = 0.0
   taper = false
   temperature = 300.0
   time = 1200.0
   timestep = [0.002 0.002 0.006 ]
   title = {str}
   trajectory = {
      center = []
      first = 0.0
      format = dtr
      frames_per_file = 250
      interval = 4.8
      name = "$JOBNAME$[_replica$REPLICA$]_trj"
      periodicfix = true
      write_last_vel = false
      write_velocity = false
   }
   transfer_asap = false
   wall_force = false
   window = {}
}