# Input Force-Field Parameters
paraTypeCharmm   on
parameters par_all27_prot_lipid.inp

#
#molecules 


set  import ions_added
set  export eqmd 

structure   ${import}.psf
coordinates ${import}.pdb
#bincoordinates  ${import}.coor
#binvelocities   ${import}.vel
#extendedSystem  ${import}.xsc

set  init_temp     0
set  desired_temp  310

#
# Output files & writing frequency for DCD
# and restart files
#

outputname       ${export}/eqmd
binaryoutput     no
restartfreq      1000
binaryrestart    yes
#dcdFile   output/solvated_heat_out.dcd

#
# Frequencies for logs and the xst file
#
outputEnergies    100
outputTiming      100
outputPressure    100
xstFreq           1000
dcdFreq           1000

#
# Timestep & friends
#

timestep 1.0 ;# 1fs/step
nonbondedFreq  1
rigidBonds   all
rigidTolerance 0.00000001
fullElectFrequency 4
stepspercycle  20


#
# Simulation space partitioning
#
switching  on
switchDist 10
cutoff  12
pairlistdist 16

#
# Basic dynamics
#
temperature  $init_temp 
COMmotion  no
dielectric 1.0
exclude  scaled1-4
1-4scaling 1.0


#
# Particle Mesh Ewald parameters.
#

PME yes
PMEGridSizeX 54
PMEGridSizeY 54
PMEGridSizeZ 75

#
# Periodic boundary things
#
wrapWater  on
wrapNearest  on
wrapAll   on

margin 3


cellBasisVector1  52.45 0 0 
cellBasisVector2  0 51.35 0
cellBasisVector3  0 0 74.67
cellOrigin       -22.69 -22.61 -0.76

#
# Fixed atoms for initial heating-up steps
#
fixedAtoms on
fixedAtomsForces on
fixedAtomsFile fix_backbone.pdb
fixedAtomsCol  B

# Restrained atoms for initial heating-up steps
#
constraints on
consRef    restrain_ca.pdb
consKFile  restrain_ca.pdb
consKCol B

#
# Langevin dynamics parameters
#
langevin on
langevinDamping  1
langevinTemp $desired_temp  # 
langevinHydrogen on

langevinPiston on
langevinPistonTarget 1.01325
langevinPistonPeriod 200
langevinPistonDecay  100
langevinPistonTemp $desired_temp  # 

useGroupPressure yes

# The actual minimisation and heating-up

# run one step to get into scripting mode
minimize 0

# turn off pressure control until later
langevinPiston off

# minimize nonbackbone atoms
minimize  2500  ;# 
output    ${export}/min_fix

#
# min all atoms
#
fixedAtoms off
minimize   2500  ;# 
output     ${export}/min_all

#
# heat with Ps restrained
#
set temp $init_temp;
while { $temp <= $desired_temp } {  ;# 
langevinTemp $temp
run 10000  ;# 
output    ${export}/heating_Pr
set temp [expr $temp + 31]
}

#
# equilibrate volume with Ps restrained
#
langevinPiston  on
run 100000 ;#
output ${export}/equil_Pr

#
# equilibrate volume without restraints
#
constraintScaling  0
run  500000 ;#
output ${export}/equil