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

#Input 
bincoordinates pSic1-pack.4rs.restart.coor 
binvelocities  pSic1-pack.4rs.restart.vel 
extendedSystem pSic1-pack.4rs.restart.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-pack.4
outputname              $output
dcdfile                 ${output}.dcd
xstFile                 ${output}.xst
dcdfreq                 500
xstFreq                 100

binaryoutput            no
#binaryrestart           no
outputEnergies          2
restartfreq             1000
outputTiming		    500


## SIMULATION PARAMETERS                                  

#constraints

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

constraints 		on
consref			pack.ref
conskfile		pack.ref
conskcol		B

set temperature         310
#temperature             $temperature;  # initial temperature

reassignFreq		1000
reassignTemp		2	
reassignIncr		2	
reassignHold		310

# AMBER FF settings
amber on
rigidBonds     none
#useSettle      on 
#rigidTolerance 1.0e-8 
cutoff         13.0 
pairlistdist   14.5
margin         10 
switching      on 
switchdist	   10
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     0.5     ;# 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  

wrapNearest        on
wrapAll            on
wrapWater          on

## EXECUTION SCRIPT     

minimize 50
run 200000