# Initialize files.
paraTypeCHARMm on
parameters par_all27_prot_lipid.prm; # Remember to enter the filename here!!
structure ../final.psf; # Remember to enter the filename here!!
coordinates ../final.pdb; #According to the UG
#velocities ./output/minimize.vel; # Remember to enter the filename here!!
temperature 0; # Had problems with initial velocities.

# Output files
outputname ./output/minimize-2k
binaryoutput no

# Trajoricity save files
#DCDfile ./traj/dynamics
#DCDfreq 100

# Restart save files
restartSave yes
restartFreq 500
restartName ./minimize/min-restart
binaryRestart yes

#
#	Approximations and parameters of the simulation
#
#

# Approximations
exclude scaled1-4
1-4scaling 1.0
switching on
switchdist 10
cutoff 12
pairlistdist 14
timestep 1.0;  # in fs.
nonbondedFreq 2


# vmd > atomselect top {protein}
# atomselect0
# vmd > measure minmax atomselect0 # -> structure contains ONLY the protein.
# {-35.3030014038 -28.7700004578 -35.2770004272} {21.7339992523 28.454000473 32.5340003967}
# Choosing 10A outside of each of these...
# Periodic boundary conditions
cellBasisVector1 80.0 0.0 0.0
cellBasisVector2 0.0 80.0 0.0
cellBasisVector3 0.0 0.0 90.0 
cellOrigin -45 -40 -45
wrapAll on

# PME for calculating electrostatics, grid same size as periodic BC grid
PME on
PMEGridSizeX 80; # grid-pts along cellBasisVector1.
PMEGridSizeY 80; # along cellBasisVector2.
PMEGridSizeZ 90; # along cellBasisVector3.

#
#	Paremeters specific to the dynamics
#
#

# Recived errors for making piston too small.  We should be increasing temp under constant volume.
# Cell is a constant volume, and there is nothing more specific in teh manual, so tryign with piston commented.

# Nose-Hoover Langevin piston used for constant pressure while increasing temperature.
# Used with periodic boundary conditions, and the algorithim increaces, or decreases the
# size of the box as necessary to maintain constant pressure.
#langevinPiston on
#langevinPistonTarget 1.01325; # P in bar, 1 ATM at sea level is 1.01325 bar.
#langevinPistonPeriod 200; # units of time in fs
#langevinPistonDecay 200
#langevinPistonTemp 300

# Constratin harmonics of the protein for the first few runs
#fixedAtoms on
#fixedAtomsFile CONS.pdb; #The entire protein is constrained when using this file...
#fixedAtomsCol B

# Increase temperature to 300K using temperature reassignments
#reassignTemp 0;   #initial temp in K
#reassignFreq 10
#reassignIncr 1;  #temp is raised by this amount in K
#reassignHold 300; #final temp in K

# Since we reassign the tmep by 1 degree K every 10 steps, we need 300 * 10 = 3000 steps to heat the system
#run 3000

minimization on
minBabyStep 1.0e-3
minTinyStep 1.0e-7
minimize 2000