set k 1
######################################################
## INPUT AND OUTPUT FILES                           ##
######################################################
set inputname    ../run8/out_eq 
set outputname   out_eq
#Onceki run'in coordinatlari
bincoordinates   $inputname.restart.coor
binvelocities    $inputname.restart.vel
extendedSystem   $inputname.restart.xsc
set ref_smd      ../common/smd0.ref
set ref_res      ../common/refressmd_$k.pdb
set ref_fix      ../common/reffix.pdb
coordinates      ../common/refcrd.pdb
structure        ../common/ref.psf
parameters       ../common/par_all27_prot_lipid.inp

######################################################
## INPUT SETTINGS                                   ##
######################################################
firsttimestep 0     
set temperature    300
set smd   1
set cons  1
set start 0

######################################################
## JOB DESCRIPTION                                  ##
######################################################

#############################################################
## SIMULATION PARAMETERS                                   ##
#############################################################

# Input
paraTypeCharmm	    on
#Bir onceki runi kulandigim icin temperature define etmemek gerekir
#temperature         $temperature
binaryoutput        yes

# Force-Field Parameters
exclude             scaled1-4
1-4scaling          1.0
cutoff              12.
switching           on
switchdist          10.
pairlistdist        13.5

# Integrator Parameters
timestep            2.0  ;# 2fs/step
rigidBonds          water  ;# needed for 2fs steps
nonbondedFreq       1
fullElectFrequency  1  
stepspercycle       1

# for periodic boundary conditions
cellBasisVector1  98.9 0.0 0.0  
cellBasisVector2  0.0 89.4 0.0
cellBasisVector3  0.0 0.0 94.6
cellOrigin 29.1 14.5 2.9
wrapAll on
DCDUnitCell     yes
#margin 5

PME on
PMEGridSizeX 100 # grid-pts along cellBasisVector1.
PMEGridSizeY 90 # along cellBasisVector2.
PMEGridSizeZ 100 # along cellBasisVector3
# use numbers with small integer factors: 2,3,5.


# Constant Temperature Control
langevin            on    ;# do langevin dynamics
langevinDamping     5     ;# damping coefficient (gamma) of 5/ps
langevinTemp        300
langevinHydrogen    off    ;# don't couple langevin bath to hydrogens

# Constant Presssure control
LangevinPiston         on
LangevinPistonTarget   1.0
LangevinPistonPeriod   200
LangevinPistonDecay    100
LangevinPistonTemp     300
useGroupPressure       yes
useFlexibleCell        yes 
useConstantArea        yes
useConstantRatio       no


# Output
outputName          $outputname

restartfreq         500 ;# 500steps = every 1ps
dcdfreq             500
xstFreq             500
outputEnergies      100
outputPressure      100
#velDCDfile					vel.dcd
#velDCDfreq          500
#############################################################
## EXTRA PARAMETERS                                        ##
#############################################################
#fixed atoms kulanmıyoruz artik
fixedAtoms off
fixedAtomsForces off
fixedAtomsFile $ref_fix
fixedAtomsCol B

if {$smd == 0} {
	SMD off
} else {
	SMD on
	
SMDFile $ref_smd
SMDDir 1   0  0
SMDk  760.00	#30 kcal/mole/A^2
SMDVel 0.005  # 0.A/ps
SMDOutputFreq 1
}

#constrain koyuyorum
if {$cons == 1} {
        constraints on
	consexp 2
	consref   $ref_res
	conskfile $ref_res
	conskcol O
	selectConstraints on
	selectConstrX off
	selectConstrY on
	selectConstrZ on
} else {
        constraints off
}


IMDon on
IMDport 3111
IMDfreq 1

#############################################################
## EXECUTION SCRIPT                                        ##
#############################################################

# Minimization

if {$start == 1} {
 	minimize 200;
}
run  500000 ;# 500000ps