# Second run of the Cyt C2:
# Reads previous trajectory file and recomputes
# electrostatic energy at each frame for the new charges.  



set outputname          cytrun2

#firsttimestep           1

# input
structure               cyt_deltaQ.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
# since PME is not allowed with pair interactions
# we normally would want a larger cutoff than usual 12.0
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
#
# these parameters are modified to be able to
# read the dcd file at each frame
#
# stepspercycle needs to be a divisor of firstTimeStep
 
timestep        	1.0
nonbondedFreq           1
fullElectFrequency      1  
stepspercycle       	1

# 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
# No PME for pair interactions
#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



# not used
pairInteraction on
pairInteractionFile  cyt_ox_beta.pdb
pairInteractionGroup1  1
pairInteractionGroup2  2
#pairInteractionSelf    on

###
coorfile open dcd cytreduced.dcd

set ts 0
while { [coorfile read] != -1 } {
  incr ts
  firstTimestep $ts
   run 0
}
coorfile close