## OUTPUT/INPUT                                          
# Amber/(t,s,x)leap generated parm and crd file  
parmfile       6pSic1_tip4.prmtop
coordinates    6pSic1_tip4.pdb  
#ambercoor      xyz

# Input 
set inputname  pSic1-tip4-run.test.7rs4.restart
bincoordinates $inputname.coor 
binvelocities  $inputname.vel 
extendedSystem $inputname.xsc 

#########################################################
proc get_first_ts { xscfile } {
  set fd [open $xscfile r]
  gets $fd
  gets $fd
  gets $fd line
  set ts [lindex $line 0]
  close $fd
  return $ts
}

set firstts [get_first_ts $inputname.xsc]
########################################################


# output
set output              pSic1-tip4-run.test.7rs5
outputname              $output
dcdfile                 ${output}.dcd
xstFile                 ${output}.xst
dcdfreq                 1
xstFreq                 1

binaryoutput            no
#binaryrestart           no
outputEnergies          500
restartfreq             50
#outputTiming		    50


## SIMULATION PARAMETERS                                  

#constraints

fixedAtoms		off
#fixedAtomsForces	off
#fixedAtomsFile	constr.ref
#fixedAtomsCol		B

constraints 		off
#consref		pack.ref
#conskfile		pack.ref
#conskcol		B

set temperature         310
#temperature             $temperature;  # initial temperature

# AMBER FF settings
amber on
rigidBonds     none 
#useSettle      on 
#rigidTolerance 1.0e-8 
cutoff         14.0 
pairlistdist   16.5
margin         10 
switching      on 
switchdist	   12
exclude        scaled1-4 
readexclusions no 
1-4scaling     1
scnb           2.0 
zeromomentum   on 
ljcorrection   on
watermodel     tip4


# Multiple timestepping
firsttimestep           $firstts
timestep                1
stepspercycle           10
nonbondedFreq           2
fullElectFrequency      2


# Constant Temperature Control
langevin            on    ;# do langevin dynamics
langevinDamping     5     ;# damping coefficient (gamma) of 5/ps
langevinTemp        310
langevinHydrogen    off    ;# don't couple langevin bath to hydrogens

langevinPiston        on
langevinPistonTarget  1.01325 ;#  in bar -> 1 atm
langevinPistonPeriod  100.
langevinPistonDecay   50.
langevinPistonTemp    310

# PME settings 
PME                 on 
PMETolerance        1.0e-6 
PMEInterpOrder      4 
FFTWUseWisdom       no 
PMEGridSizeX        112  
PMEGridSizeY        112  
PMEGridSizeZ        96  

# periodic cell  
dcdUnitCell         yes
#cellBasisVector1   110.906  0.0 0.0 
#cellBasisVector2   -36.9688 104.5635  0.0 
#cellBasisVector3   -36.9688 -52.2818 -90.5547  
#cellOrigin         0.0 0.0 0.0

wrapNearest        on
wrapAll            on
wrapWater          on

## EXECUTION SCRIPT     

minimize 100
run 2000