The vrun Stage

Analysis
  • Overview
  • Default Configuration

This stage runs vrun with the Desmond trajectory from the last simulate stage. The vrun stage is useful for analyzing trajectories, such as calculating energies of the system for each frame.

The vrun stage can be used to analyze a previously generated trajectory. This trajectory can be either generated by the previous Desmond simulation stage or a completely different simulation run. You can call various plugins to obtain information for the trajectory. For example, the eneseq plugin can be used to calculate energies of the system for each frame. All the parameters from the simulate stage can be used with these stages, but the default settings for the following keywords are different:

trajectory = false
checkpt = off
maeff_output = off
eneseq.interval = 0.0

Setting eneseq.interval to zero means that the energy is computed for every frame of the trajectory.

The vrun_frameset keyword is used to set the path to the MD simulation trajectory that should be analyzed. For example:

vrun {
        vrun_frameset = "/home/Desmond_files/my_trj"
}

Default configurations for the vrun 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 = false
   compress = "$MAINJOBNAME_$STAGENO-out.tgz"
   coulomb_method = useries
   cpu = 1
   cutoff_radius = 9.0
   dipole_moment = false
   dir = "$[$JOBPREFIX/$]$[$PREFIX/$]$MAINJOBNAME_$STAGENO$[_lambda$LAMBDA$]"
   dryrun = false
   ebias_force = false
   effect_if = {list}
   elapsed_time = 0.0
   energy_group = false
   eneseq = {
      first = 0.0
      interval = 0.0
      name = "$JOBNAME$[_replica$REPLICA$].ene"
   }
   ensemble = NPT
   fep = {
      i_window = {int}
      lambda = "default:12"
      output = {
         first = 0.0
         interval = 1.2
         name = "$JOBNAME$[_replica$REPLICA$].dE"
      }
      trajectory = {
         record_windows = [0 -1 ]
      }
      type = small_molecule
   }
   gaussian_force = false
   glue = solute
   host = "$SUBHOST"
   jin_file = []
   jin_must_transfer_file = []
   jlaunch_opt = ["" ]
   jobname = "$MAINJOBNAME_$STAGENO$[_lambda$LAMBDA$]"
   jout = ""
   lambda_dynamics = false
   maeff_output = false
   meta = false
   meta_file = {str}
   msd = false
   prefix = ""
   pressure = 1.01325
   pressure_tensor = false
   print_expected_memory = false
   print_restraint = false
   randomize_velocity = {
      first = 0.0
      interval = inf
      seed = 2007
      temperature = "@*.temperature"
   }
   restrain = none
   restraints = {
      existing = ignore
      new = []
   }
   rnemd = false
   should_skip = false
   should_sync = true
   simbox = {
      first = 0.0
      interval = 1.2
      name = "$JOBNAME$[_replica$REPLICA$]_simbox.dat"
   }
   skip_intermediates = false
   spatial_temperature = false
   struct_output = ""
   surface_tension = 0.0
   taper = false
   temperature = 300.0
   time = 1200.0
   timestep = [0.002 0.002 0.006 ]
   title = {str}
   trajectory = false
   transfer_asap = false
   vrun_frameset = "$FRAMESET"
   wall_force = false
   window = {}
}