choderalab/yank

netcdf complex-explicit {
dimensions:
    iteration = UNLIMITED ; // (1 currently)
    replica = 13 ;
    atom = 48104 ;
    spatial = 3 ;
    scalar = 1 ;
variables:
    float positions(iteration, replica, atom, spatial) ;
        positions:units = "nm" ;
        positions:long_name = "positions[iteration][replica][atom][spatial] is position of coordinate \'spatial\' of atom \'atom\' from replica \'replica\' for iteration \'iteration\'." ;
    int states(iteration, replica) ;
        states:units = "none" ;
        states:long_name = "states[iteration][replica] is the state index (0..nstates-1) of replica \'replica\' of iteration \'iteration\'." ;
    float energies(iteration, replica, replica) ;
        energies:units = "kT" ;
        energies:long_name = "energies[iteration][replica][state] is the reduced (unitless) energy of replica \'replica\' from iteration \'iteration\' evaluated at state \'state\'." ;
    int64 proposed(iteration, replica, replica) ;
        proposed:units = "none" ;
        proposed:long_name = "proposed[iteration][i][j] is the number of proposed transitions between states i and j from iteration \'iteration-1\'." ;
    int64 accepted(iteration, replica, replica) ;
        accepted:units = "none" ;
        accepted:long_name = "accepted[iteration][i][j] is the number of proposed transitions between states i and j from iteration \'iteration-1\'." ;
    float box_vectors(iteration, replica, spatial, spatial) ;
        box_vectors:units = "nm" ;
        box_vectors:long_name = "box_vectors[iteration][replica][i][j] is dimension j of box vector i for replica \'replica\' from iteration \'iteration-1\'." ;
    float volumes(iteration, replica) ;
        volumes:units = "nm**3" ;
        volumes:long_name = "volume[iteration][replica] is the box volume for replica \'replica\' from iteration \'iteration-1\'." ;
    string timestamp(iteration) ;

// global attributes:
        :title = "Replica-exchange simulation created using ReplicaExchange class of repex.py on Sun Nov 16 22:18:46 2014" ;
        :application = "YANK" ;
        :program = "yank.py" ;
        :programVersion = "unknown" ;
        :Conventions = "YANK" ;
        :ConventionVersion = "0.1" ;

group: timings {
  variables:
      float iteration(iteration) ;
      float mixing(iteration) ;
      float propagate(iteration, replica) ;
  } // group timings

group: thermodynamic_states {
  variables:
      int64 nstates ;
      float temperatures(replica) ;
          temperatures:units = "K" ;
          temperatures:long_name = "temperatures[state] is the temperature of thermodynamic state \'state\'" ;
      string systems(replica) ;
          systems:long_name = "systems[state] is the serialized OpenMM System corresponding to the thermodynamic state \'state\'" ;
  } // group thermodynamic_states

group: options {
  variables:
      double collision_rate ;
          collision_rate:type = "float" ;
          collision_rate:units = "/picosecond" ;
      double constraint_tolerance ;
          constraint_tolerance:type = "float" ;
      double timestep ;
          timestep:type = "float" ;
          timestep:units = "femtosecond" ;
      int64 nsteps_per_iteration ;
          nsteps_per_iteration:type = "int" ;
      int64 number_of_iterations ;
          number_of_iterations:type = "int" ;
      double equilibration_timestep ;
          equilibration_timestep:type = "float" ;
          equilibration_timestep:units = "femtosecond" ;
      int64 number_of_equilibration_iterations ;
          number_of_equilibration_iterations:type = "int" ;
      string title(scalar) ;
          title:type = "str" ;
      int64 minimize ;
          minimize:type = "bool" ;
      string replica_mixing_scheme(scalar) ;
          replica_mixing_scheme:type = "str" ;
      int64 online_analysis ;
          online_analysis:type = "bool" ;
      int64 verbose ;
          verbose:type = "bool" ;
      int64 show_mixing_statistics ;
          show_mixing_statistics:type = "bool" ;
      int64 mc_atoms ;
          mc_atoms:type = "NoneType" ;
      int64 mc_displacement ;
          mc_displacement:type = "bool" ;
      int64 mc_rotation ;
          mc_rotation:type = "bool" ;
      double displacement_sigma ;
          displacement_sigma:type = "float" ;
          displacement_sigma:units = "nanometer" ;
      int64 displacement_trials_accepted ;
          displacement_trials_accepted:type = "int" ;
      int64 rotation_trials_accepted ;
          rotation_trials_accepted:type = "int" ;
  } // group options

group: metadata {
  variables:
      double standard_state_correction ;
  } // group metadata
}