The lambda_hopping Stage

Overview
Default Configuration

This stage runs a lambda hopping MD simulation on the system.

The lambda_hopping stage is a Desmond simulation stage. For more information on Desmond simulation stages, see The simulate Stage.

Table 1. Keywords for the lambda_hopping stage
Keyword	Description
`cfg_file`	This specifies the .cfg configuration file to be used for the given simulation, as an input to the Desmond engine. This keyword is not required; multisim is capable of creating and supplying the relevant .cfg file.
`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.
`atom_group`	Define atom groups within the `.cms` file (defined by the `i_ffio_grp_name` property). Atom groups can be restrained, or associated with particular thermostats. This keyword can take on the following values: `none`—Remove all atom groups. `retain`—Keep all atom groups from the previous stage. `{ atom =` atoms `index =` i `name =` name `}`—atom group block. Put the specified atoms in the atom group i that has the name name. The `atom` keyword accepts an atom list, an ASL expression prefixed by `asl:`, or keywords `heavy atom`, `solute`, `solute_heavy_atom`, `solvent`, `solvent_heavy_atom`. The index i is the value for the `i_ffio_grp_`name property. Desmond only supports index numbers from 0 to 7. `[` group1 group2 ... `]`—Specify multiple atom groups. Each group can be specified as a block, in the above format. Atom groups may also be defined in the assign_forcefield stage.

Default configurations for the lambda_hopping 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_$STAGENO"
   dryrun = false
   ebias_force = false
   effect_if = {list}
   elapsed_time = 0.0
   energy_group = false
   eneseq = {
      first = 0.0
      interval = 1.2
      name = "$JOBNAME$[_replica$REPLICA$].ene"
   }
   ensemble = NPT
   fep = {
      i_window = {int}
      lambda = "default:12"
      output = {
         first = 0.0
         interval = 1.2
         name = "$JOBNAME$[_replica$REPLICA$].dE"
      }
      trajectory = {
         record_windows = [0 -1 ]
      }
      type = small_molecule
   }
   fep_convergence = 0.0
   gaussian_force = false
   gcmc = {
      ene_name = "$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"
   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"
   }
   replica = [
      {model_file = {str}
       temperature = 300
      }

      {model_file = {str}
       temperature = 310
      }
   ]
   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"
   }
   solute_tempering = false
   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}
   total_proc = {int}
   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 = {}
}