###################################################
# UNCHARGE SODIUM ION
###################################################


# INPUT

set temp                300.0

parameters              ../common/par_all22_prot.inp
paraTypeCharmm          on

exclude                 scaled1-4
1-4scaling              1.0


# TOPOLOGY

structure               solvate.psf

# INITIAL CONDITIONS

coordinates             solvate.pdb
bincoordinates          forward.coor
binvelocities           forward.vel
extendedSystem          forward.xsc

# OUTPUT FREQUENCIES

outputenergies          100
outputtiming            100
outputpressure          100
restartfreq             100
XSTFreq                 100


# OUTPUT AND RESTART

outputname              backward
restartname             backward

binaryoutput            yes
binaryrestart           yes


# PME

PME                     yes
PMETolerance            10e-6
PMEInterpOrder          4

PMEGridSpacing          1.0

# WRAP WATER FOR OUTPUT

wrapAll                 on


# CONSTANT-T
langevin                on
langevinTemp            $temp
langevinDamping         1.0


# CONSTANT-P

LangevinPiston          on
LangevinPistonTarget    1
LangevinPistonPeriod    100
LangevinPistonDecay     100
LangevinPistonTemp      $temp

StrainRate              0.0 0.0 0.0
useGroupPressure        yes

useflexiblecell         no


# SPACE PARTITIONING

splitpatch              hydrogen
hgroupcutoff            2.8
stepspercycle           20
margin                  1.0


# CUT-OFFS

switching               on
switchdist               8.0
cutoff                   9.0
pairlistdist            10.0


# RESPA PROPAGATOR

timestep                2.0

fullElectFrequency      2
nonbondedFreq           1


# SHAKE

rigidbonds              all
rigidtolerance          0.000001
rigiditerations         400


# COM

commotion               no


# FEP PARAMETERS

source                  ../tools/fep.tcl

alch                    on
alchType                FEP
alchFile                solvate.fep
alchCol                 B
alchOutFile             backward.fepout
alchOutFreq             10

alchVdwLambdaEnd        0.0
alchElecLambdaStart     0.0
alchVdWShiftCoeff       5.0
alchDecouple            on

alchEquilSteps          100
set numSteps            500

runFEP 1.0 0.0 -0.0625 $numSteps