# First run of the Cyt C2:
# Generates a trajectory file by writing to DCD at every frame
#  

#contfrom 		1

set outputname          cytreduced

#firsttimestep           1

# input
structure               cyt_reduced.psf
coordinates             SPH_1CXCequi.pdb

if {1} {
set inputname		cyt_red_init
bincoordinates          $inputname.rst.coor
ExtendedSystem          $inputname.rst.xsc          
binvelocities           $inputname.rst.vel
}


paraTypeCharmm          on
parameters              par_all27_prot_lipid_mod.inp      

numsteps                200
#minimization            off  

if {0} {
temperature             298.0
}

#fixedAtoms              off

# force field parameters
exclude         scaled1-4
1-4scaling      1.0
cutoff          12.0
switching       On
switchdist      10.0
pairlistdist        14.0

# integrator params
# Since we want to keep track of energies at every frame we want  
# to do the unsual practice of setting the below frequencies all to 1 
timestep        1.0
nonbondedFreq           1
fullElectFrequency      1  
stepspercycle       10

# Periodic boundary condition

if {0} {
cellBasisVector1        53 0 0
cellBasisVector2        0 51 0
cellBasisVector3        0 0 51
cellorigin              0 0 0
}

wrapWater               on
wrapAll                 on
wrapNearest             on

# Particle Mesh Ewald
PME                     yes
PMEGridsizeX            54
PMEGridsizeY            54
PMEGridsizeZ            54

# Temperature coupling
langevin                on     # do langevin dynamics
langevinDamping         10     # damping coefficient (gamma) of 5/ps
langevinTemp            298    # bath temperature
#langevinHydrogen        no     # don't couple langevin bath to hydrogens

# Pressure coupling
useFlexibleCell         yes
useConstantRatio        yes
langevinPiston          on
langevinPistonTarget    1.01325 #  in bar -> 1 atm
langevinPistonPeriod    200
langevinPistonDecay     200
langevinPistonTemp      298.0
#fixedAtomsForces        off

# Harmonic constraints
#constraints             on
#consexp                 4
#consref                 $inputcoor
#conskfile               $inputcoor
#conskcol                B


# output
#
# Again, for keeping track of energies at each time frame we will
# output at every step
#
outputname              $outputname
dcdfile                 $outputname.dcd
XSTfile                 $outputname.xst
binaryoutput            no
outputEnergies          1
dcdfreq                 1
XSTfreq                 200

restartname             $outputname.rst                 
restartfreq             200