# YASARA MACRO
# TOPIC:       3. Molecular Dynamics
# TITLE:       Play back a molecular dynamics trajectory
# REQUIRES:    Dynamics
# AUTHOR:      Elmar Krieger
# LICENSE:     GPL
# DESCRIPTION: This macro plays back a molecular dynamics simulation, looping back to the start.

# You can either set the target structure by clicking on Options > Macro > Set target,
# or by uncommenting the line below and specifying it directly.
#MacroTarget = 'c:\MyProject\1crn'

# Set playback waittime (1 is maximum playback speed)
waittime=12

# Choose trajectory format, sim or xtc
format='sim'

# Forcefield to use (these is a YASARA commands, so no '=' used)
ForceField AMBER03

# In case the simulation was run without 'CorrectDrift on' and the solute diffused
# through a periodic boundary, you can keep it centered here by specifying the number
# of an atom close to the core of the solute, which will be kept at the cell center.
central=0

# No changes required below this point!

# Speed up playback using short dummy cutoff and no longrange forces
Cutoff 2.62
Longrange None
# Do we have a target?
if MacroTarget==''
  RaiseError "This macro requires a target. Either edit the macro file or click Options > Macro > Set target to choose a target structure"
# Do we have a scene with water?
scene = FileSize (MacroTarget)_water.sce
if not scene
  RaiseError 'Could not find initial scene file (MacroTarget)_water.sce. Click Options > Macro > Set target and choose the target structure for which a simulation has been run before'
# Load the scene
LoadSce (MacroTarget)_water
# Pick a nice style
Style Backbone=Ribbon,Sidechain=Stick
Console off
i=00000
filename = '(MacroTarget)(i).(format)'
while 1
  if format=='sim'
    # See if next snapshot is present
    sim = FileSize (MacroTarget)(i).sim
    if not sim
      # Loop back to start
      i=00000
    # Load the snapshot
    LoadSim (MacroTarget)(i)
    i=i+1
  else
    i=i+1
    last = LoadXTC (filename),(i)
    if last
      # Loop back to start
      i=00000
  # Show the simulation time
  simtime=Time
  ShowMessage 'Current simulation time is (0+simtime/1000) picoseconds.'
  if central
    # Keep a chosen atom at the center of the cell (Cell returns center as values 7-9) 
    _,_,_,_,_,_,cen() = Cell
    pos() = PosAtom (central)
    MoveAtom all,(cen-pos)
  # Make sure that the simulation does not continue while we wait
  Sim Pause
  # Wait a bit
  Wait (waittime)