###################################################
#  FORWARD DECOUPLE ON
###################################################


# INPUT
set runID		MYRUNID	
set window		MYWINDOW
set name	 	SOD_w	
set inputname		aqua-equil	
set temperature         310.0
set RefPDB		${name}.pdb
set outputName		${name}_win${window}_fw${runID}


parameters              ../par_all27_prot_na_NBFIX.prm
paraTypeCharmm          on

exclude                 scaled1-4
1-4scaling              1.0


# TOPOLOGY

structure               ../${name}.psf

# INITIAL CONDITIONS

coordinates             ../${name}.pdb
bincoordinates          ../${inputname}.coor
binvelocities           ../${inputname}.vel
extendedsystem          ../${inputname}.xsc

# OUTPUT FREQUENCIES

outputenergies          1000
outputtiming            1000
outputpressure          1000
restartfreq             1000
XSTFreq                 1000
dcdFreq			1000

# OUTPUT AND RESTART

outputname              $outputName 
restartname             $outputName

binaryoutput            yes
binaryrestart           yes

# CONSTANT-T
langevin                on
langevinTemp            $temperature
langevinDamping         1.0

# PME

PME                     yes
PMETolerance            10e-6
PMEInterpOrder          4

PMEGridSpacing          1.0

# Periodic Boundary Conditions
#cellBasisVector1    30.0    0.   0.
#cellBasisVector2     0.    30.0   0.
#cellBasisVector3     0.    0    30.0
#cellOrigin          0.0 0.0 0.0


# WRAP WATER FOR OUTPUT

wrapAll                 on

# CONSTANT-P

LangevinPiston          on
LangevinPistonTarget    1.01325
LangevinPistonPeriod    200
LangevinPistonDecay     50
LangevinPistonTemp      $temperature
#StrainRate              0.0 0.0 0.0
useGroupPressure        yes
useFlexibleCell         no 
useConstantArea         no

# SPACE PARTITIONING

stepspercycle           20
#margin                  1.0

# CUT-OFFS

switching               on
switchdist              10.0
cutoff                  12.0
pairlistdist            13.5
#LJCorrection		on  ;# don't use this in FEP

# RESPA PROPAGATOR

timestep                2.0
fullElectFrequency      2
nonbondedFreq           1


# SHAKE

rigidbonds              all
rigidtolerance          0.000001
rigiditerations         400


# COM

ComMotion            no


# FEP PARAMETERS

source                  ../fep.tcl

alch                    on
alchType                FEP
alchFile                ../${name}.fep
alchCol                 B
alchOutFile             ${name}_win${window}_fw${runID}.fepout
alchOutFreq             10

alchVdwLambdaEnd        0.5 ;# vdw is fully coupled until 0.5 
alchElecLambdaStart     0.5
alchVdWShiftCoeff       5.0
alchDecouple            on

alchEquilSteps          250000
set totalFEPsteps       500000


#set currentLambda [expr {$dLambda*($window-1)}]
#set nextLambda    [expr {$currentLambda + $dLambda}]
#set nextLambda    [expr int($nextLambda*1000)/1000.] ;# change 1.E-9 to 0.0

set currentLambda	[expr double(MYL0)]
set nextLambda		[expr double(MYL1)]
set LambdaList    [list $currentLambda $nextLambda]

alchLambda	$currentLambda
alchLambda2	$nextLambda
minimize	800
reinitvels	$temperature

runFEPlist $LambdaList $totalFEPsteps