########################
#MD Prep of Config File#
########################
set outname "OUTNAME"
set inputname "INNAME"
set names [list \
_LipMelt Lipid-Melt.conf \
_ProtConst Protein-Constrained.conf \
_BackConst Backbone-Constrained.conf \
_Equil Equilibration.conf \
_Produc Production.conf \
]
foreach {ending conf} $names {
	puts "debug"
	set ofile [open $conf w]
	puts $ofile [format "structure\t\t$outname\_popcwi.psf"]
	puts $ofile [format "coordinates\t\t$outname\_popcwi.pdb"]
	puts $ofile [format "outputName\t\t$outname$ending\n"]
	if {$ending == "_LipMelt"} {
		puts $ofile [format "temperature\t\t300\n"]
		puts $ofile "if {0} \{"
	} else {
		puts $ofile [format "temperature\t\t310\n"]
		puts $ofile "if {1} \{"
	}
	puts $ofile [format "set inputname\t\t$outname$ending"]
	puts $ofile [format "binCoordinates\t\t$inputname\.restart.coor"]
	puts $ofile [format "binVelocities\t\t$inputname\.restart.vel"]
	puts $ofile [format "extendedSystem\t\t$inputname\.restart.xsc\n\}\n"]
	puts $ofile [format "firsttimestep\t\t0\n"]
	puts $ofile [format "paraTypeCharmm\t\ton"]
	puts $ofile [format "parameters\t\t/home/bassam/Topology\ and\ Parameters/par_all36m_prot.prm"]
	puts $ofile [format "mergeCrossterms\t\tyes"]
	puts $ofile [format "parameters\t\t/home/bassamh/Topology\ and\ Parameters/par_all36_lipid.prm"]
	puts $ofile [format "parameters\t\t/home/bassamh/Topology\ and\ Parameters/toppar_water_ions_namd.str"]
	puts $ofile [format "parameters\t\t/home/bassamh/Topology\ and\ Parameters/par_all36_cgenff.prm"]
	puts $ofile [format "parameters\t\t/home/bassamh/Topology\ and\ Parameters/par_all36_carb.prm"]
	puts $ofile [format "parameters\t\t/home/bassamh/Topology\ and\ Parameters/cAMP.prm\n"]
	puts $ofile [format "temperature\t\t \$temperature\n"]
	if {$ending == "_LipMelt"} {
		puts $ofile "if \{1} \{"
	} else {
		puts $ofile "if \{0} \{"
	}
	puts $ofile [format "cellBasisVector1\t0.\t0.\t0."]
	puts $ofile [format "cellBasisVector2\t0.\t0.\t0."]
	puts $ofile [format "cellBasisVector3\t0.\t0.\t0."]
	puts $ofile [format "cellOrigin\t\t0.\t0.\t0.\n\}\n"]
	puts $ofile [format "wrapWater\t\toff"]
	puts $ofile [format "wrapAll\t\t\toff\n"]
	puts $ofile "# Force-Field Parameters"
	puts $ofile [format "exclude\t\t\tscaled1-4"]
	puts $ofile [format "1-4scaling\t\t1.0"]
	puts $ofile [format "cutoff\t\t\t12.0"]
	puts $ofile [format "switching\t\ton"]
	puts $ofile [format "switchdist\t\t10.0"]
	puts $ofile [format "pairlistdist\t\t13.5\n"]
	puts $ofile "# Integrator Parameter"
	puts $ofile [format "timestep\t\t2.0"]
	puts $ofile [format "rigidBonds\t\tall"]
	puts $ofile [format "nonbondedFreq\t\t1"]
	puts $ofile [format "fullElectFrequency\t4\t;# product of this and timestep must not exceed 8 (leave this @ 4)"]
	puts $ofile [format "stepspercycle\t\t20\n"]
	puts $ofile [format "PME\t\t\ton"]
	puts $ofile [format "PMEGridSpacing\t\t1.0\n"]
	puts $ofile "# Constant Temperature"
	puts $ofile [format "langevin\t\ton"]
	puts $ofile [format "langevinDamping\t\t1"]
	puts $ofile [format "langevinTemp\t\t\$temperature\n"]
	puts $ofile "# Constant Pressure"
	if {$ending == "_LipMelt"} {
		puts $ofile "if \{0} \{"
	} else {
		puts $ofile "if \{1} \{"
	}
	puts $ofile [format "useGroupPressure\tyes ;# needed for 2fs steps"]
	puts $ofile [format "useFlexibleCell\t\tyes ;# no for water box, yes for membrane"]
	puts $ofile [format "useConstantArea\t\tyes ;# no for water box, yes for membrane\n"]
	puts $ofile [format "langevinPiston\t\ton"]
	puts $ofile [format "langevinPistonTarget\t1.01325 ;# in bar --> 1 atm"]
	puts $ofile [format "langevinPistonPeriod\t200.0"]
	puts $ofile [format "langevinPistonDecay\t50.0"]
	puts $ofile [format "langevinPistonTemp\t\$temperature\n\}\n"]
	puts $ofile [format "restartfreq\t\t5000"]
	puts $ofile [format "dcdfreq\t\t\t1000"]
	puts $ofile [format "xstfreq\t\t\t1000"]
	puts $ofile [format "outputEnergies\t\t500"]
	puts $ofile [format "outputPressure\t\t500\n"]
	puts $ofile "# Steered MD"
	puts $ofile [format "SMD\t\t\ton"]
	puts $ofile [format "SMDFile\t\t\tlip-ref.pdb"]
	puts $ofile [format "SMDVel\t\t\t0"]
	puts $ofile [format "SMDk\t\t\t5"]
	puts $ofile [format "SMDDir\t\t\t0 0 -1"]
	puts $ofile [format "SMDOutputFreq\t\t10000\n"]
	puts $ofile "# Steered restraint for cAMP"
	puts $ofile [format "colvars\t\t\ton"]
	puts $ofile [format "colvarsConfig\t\tcAMP-SMD.in\n"]
	puts $ofile "# Constrained Atoms (prevent drift from SMD...only restraining CA from resid 208)"
	if {$ending == "_ProtConst" || $ending == "_BackConst"} {
		puts $ofile "if \{1} \{"
	} else {
		puts $ofile "if \{0} \{"
	}
	puts $ofile [format "constraints\t\toff"]
	puts $ofile [format "consexp\t\t\t2"]
	puts $ofile [format "consref\t\t\tSMD.pdb"]
	puts $ofile [format "conskfile\t\tSMD.pdb"]
	puts $ofile [format "conskcol\t\tB\n\}\n"]
	puts $ofile "# Minimization"
	puts $ofile "if \{1} \{"
	puts $ofile [format "minBabyStep\t\t1.0e-3"]
	puts $ofile [format "minimize\t\t1000"]
	puts $ofile [format "reinitvels\t\t\$temperature\n\}\n"]
	if {$ending == "_LipMelt"} {
		puts $ofile "run 1000000 ;# 2 ns"
	} if {$ending == "_ProtConst" || $ending == "_BackConst"} {
		puts $ofile "run 2000000 ;# 4 ns"
	} else {
		puts $ofile "run 5000000 ;# 10 ns"
	}
	close $ofile
}