set MOL ethane
set temp [expr 37+273.15]
set boxx 21.7000
set boxy 21.7000
set boxz 21.7000

structure ${MOL}.psf 
coordinates ${MOL}.0.pdb 
temperature 0 
parameters par_all27_prot_na.prm 
paraTypeCharmm on

outputEnergies  500
outputTiming    500
xstFreq         500
dcdFreq         1000
wrapAll         on
wrapNearest     on

rigidbonds      all
timestep        2
nonBondedFreq   1
fullElectFrequency 1
stepsPerCycle   20

switching       on
switchDist      8
cutoff          12
pairlistdist    14

outputname ${MOL}-equil
binaryoutput off

restartname ${MOL}.0
restartfreq 500

numsteps 90000000

#########################################
cellBasisVector1        $boxx   00.00   00.00
cellBasisVector2        00.00   $boxy   00.00
cellBasisVector3        00.00   00.00   $boxz


#########################################
Pme             on
PmeGridsizeX    25
PmeGridsizeY    25
PmeGridsizeZ    25

exclude         scaled1-4
1-4scaling      1.0

########################################
# PRESSURE AND TEMPERATURE CONTROL
#########################################

langevin                on
langevinDamping         10
langevinTemp            $temp
langevinHydrogen        no

langevinPiston          on
langevinPistonTarget    1.01325
langevinPistonPeriod    200
langevinPistonDecay     100
langevinPistonTemp      $temp

useFlexibleCell no
useGroupPressure        yes     #THIS WILL ALLOW THE SYSTEM SMALLER FLUCTUATIONS


#########################################
# FEP
#########################################

source fep.tcl

fep		on
fepFile		${MOL}.fep
fepCol		B
fepOutFile	${MOL}.fepout
fepOutFreq	10
fepEquilSteps	500
fepElecLambdaStart 0.5
fepVdwLambdaEnd 1.0
decouple on 

# Block for minimization and heating
lambda 0
lambda2 0

#########################################
#Minimize
#########################################

minimize 300

#########################################
# HEAT
#########################################

set tem 70.14;
while { $tem < $temp } { 
 langevinTemp $tem
 run 5000
 output ${MOL}-heat
 set tem [expr $tem + 30]
}
langevinTemp $temp
run 100000

set nSteps	15000
set dLambda	0.01

set init { 1e-10 0.0000001 0.000001 0.00001 0.0001 0.001 0.01  }
set end  { 0.99 0.999 0.9999 0.99999 0.999999 0.9999999 0.999999999}

runFEPlist $init $nSteps
runFEP 0.01 0.99 $dLambda $nSteps
runFEPlist $end  $nSteps