# 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'

# Forcefield to use (these are all YASARA commands, so no '=' used)
ForceField Amber99

# Cell boundary
Boundary periodic

# Set playback waittime (1 is maximum playback speed)
waittime = 25

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

# Set to 1 if you want to center the structure in every frame to keep it from
# crossing a periodic boundary. Use *only if absolutely needed*, since it may
# cause an error message about a 'search grid overflow'. Also this only works
# as long as a small part of the structure really crosses a boundary.
centered = 0

# 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'

# 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 centered
    # We want to keep the protein at the center of the cell
    # Get cell center in cellinfo(7)-cellinfo(9) and the mean solute position in x,y,z
    cellinfo() = Cell
    x,y,z = PosAtom !Hetgroup,mean=Yes
    # Move everything back
    MoveAtom all,(cellinfo(7)-x),(cellinfo(8)-y),(cellinfo(9)-z)
    # Moving atoms around stops the simulation, restart
    OnError Continue
    Sim On
    OnError Stop
    Time (simtime)
  # Make sure that the simulation does not continue while we wait
  Sim Pause
  # Wait a bit
  Wait (waittime)