#############################################################
## Get Total Energy of Ubiquitin                           ##
#############################################################

# This script runs namd for 0 steps for the ubiquitin system 
# with everything fixed exept the protein.
# Loops through all frames of a trajectory and akes them as 
# initial coordinates. 
# The output of each run contains then the energies of the
# protein only for that configuration.

#############################################################
## ADJUSTABLE PARAMETERS                                   ##
#############################################################

structure          ../common/ubq.psf
coordinates        ../common/ubq.pdb
outputName         ubq-get-energy

set temperature    310

# Continuing a job from the restart files
if {0} {
set inputname      ubq-nvt
binCoordinates     $inputname.restart.coor
binVelocities      $inputname.restart.vel  ;# remove the "temperature" entry if you use this!
extendedSystem	   $inputname.restart.xsc
} 

firsttimestep      0


#############################################################
## SIMULATION PARAMETERS                                   ##
#############################################################

# Input
paraTypeCharmm	    on
parameters          ../common/par_all27_prot_lipid.inp 

# NOTE: Do not set the initial velocity temperature if you 
# have also specified a .vel restart file!
temperature         $temperature
 

# Periodic Boundary conditions
# NOTE: Do not set the periodic cell basis if you have also 
# specified an .xsc restart file!
if {0} { 
cellBasisVector1    20.    0.   0.
cellBasisVector2     0.   20.   0.
cellBasisVector3     0.    0   50.
cellOrigin           0.    0.   0.
}
wrapWater           on
wrapAll             on


# Force-Field Parameters
exclude             scaled1-4
1-4scaling          1.0
cutoff              12.
switching           on
switchdist          10.
pairlistdist        13.5


# Integrator Parameters
timestep            2.0  ;# 2fs/step
rigidBonds          all  ;# needed for 2fs steps
nonbondedFreq       1
fullElectFrequency  2  
stepspercycle       10


#PME (for full-system periodic electrostatics)
if {0} {
PME                 yes
PMEGridSizeX        32
PMEGridSizeY        32
PMEGridSizeZ        64
}


# Constant Temperature Control
if {0} {
langevin            on    ;# do langevin dynamics
langevinDamping     5     ;# damping coefficient (gamma) of 5/ps
langevinTemp        $temperature
langevinHydrogen    no    ;# don't couple langevin bath to hydrogens
}

# Constant Pressure Control (variable volume)
if {0} {
useGroupPressure      yes ;# needed for 2fs steps
useFlexibleCell       no  ;# no for water box, yes for membrane
useConstantArea       no  ;# no for water box, yes for membrane

langevinPiston        on
langevinPistonTarget  1.01325 ;#  in bar -> 1 atm
langevinPistonPeriod  100.
langevinPistonDecay   50.
langevinPistonTemp    $temperature
}


#restartfreq         500     ;# 500steps = every 1ps
#dcdfreq             500
#xstFreq             500
outputEnergies      1
outputPressure      1


# Fixed Atoms Constraint (set PDB beta-column to 1)
if {0} {
fixedAtoms          on
fixedAtomsFile      myfixedatoms.pdb
fixedAtomsCol       B
}


# IMD Settings (can view sim in VMD)
if {0} {
IMDon           on
IMDport         3000    ;# port number (enter it in VMD)
IMDfreq         1       ;# send every 1 frame
IMDwait         no      ;# wait for VMD to connect before running?
}


#############################################################
## EXTRA PARAMETERS                                        ##
#############################################################

# Put here any custom parameters that are specific to 
# this job (e.g., SMD, TclForces, etc...)



#############################################################
## EXECUTION SCRIPT                                        ##
#############################################################



# runs 0 time steps for each frame in the dcd 

# opens the dcd file to read the coordinates
coorfile open dcd ubq-nvt-prot.dcd

# runs 0 time steps for each frame in the dcd


set i 0
while { ![coorfile read] } {
  incr i 50   ;#since the dcd was saved every 50 steps in the ubq-nvt simulation
  firsttimestep $i
  run 0
}

coorfile close


# Minimization
if {0} {
minimize            100
reinitvels          $temperature
}

#run 500000 ;# 1 ns