#######################
#
#       Methane to nada
#
#######################


# MD SETUP

timestep                2.0
#numsteps                10
# numsteps is required but will be ignored


# FLEXIBLE CELL

useflexiblecell         no


# INPUT

structure               ../solvate.psf 
parameters              ../../common/par_all22_prot.inp
paraTypeCharmm          on

coordinates             ../solvate.pdb

bincoordinates          ../thermalize.coor
binvelocities           ../thermalize.vel


# EXTENDED SYSTEM

extendedSystem          ../thermalize.xsc


# OUTPUT

outputenergies          100
outputtiming            100
outputpressure          100
binaryoutput            no

outputname              alchemy_1
restartname             alchemy_1
restartfreq             100
binaryrestart           yes

XSTFreq                 100


# PME

PME                     yes
PMETolerance            10e-6
PMEInterpOrder          4

PMEGridSizeX            32
PMEGridSizeY            32
PMEGridSizeZ            32


# WRAP WATER FOR OUTPUT

wrapWater               on


# CONSTANT-T

langevin                on
langevinTemp            300
langevinDamping         1.0


# CONSTANT-P

LangevinPiston          on
LangevinPistonTarget    1
LangevinPistonPeriod    100
LangevinPistonDecay     150
LangevinPistonTemp      300
useGroupPressure        yes


# SPACE PARTITIONING

splitpatch              hydrogen
hgroupcutoff            2.8
stepspercycle           20
margin                  1.0


# CUT-OFFS

switching               on
switchdist              8.0
cutoff                  10.0
pairlistdist            12.0


# RESPA 

fullElectFrequency      2
nonbondedFreq           1


# 1-4 NON-BONDED

exclude                 scaled1-4
1-4scaling              1.0


# COM

commotion               no


# SHAKE

rigidbonds              all 


# FEP

source ../FEP_tools/fep.tcl

alch                 on
alchType             fep
alchFile             decouple.fep
alchCol              B
alchOutFreq          10
alchOutFile          decouple-forward.fepout

alchVdwLambdaEnd     1.0
alchElecLambdaStart  0.5
alchVdWShiftCoeff    5.0
alchDecouple         yes

alchEquilSteps       2500
set nSteps           52500

runFEP         0.0   1.0   0.1      $nSteps
runFEP         1.0   0.0  -0.1      $nSteps