structure          ubq.psf
coordinates        ubq.pdb

set temperature    310
set outputname     ubq_output

firsttimestep      0

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

# Input
paraTypeCharmm      on
parameters          par_all27_prot_lipid.inp 
temperature         $temperature


# 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


# Constant Temperature Control
langevin            off    ;# do langevin dynamics
langevinDamping     5     ;# damping coefficient (gamma) of 5/ps
langevinTemp        $temperature
langevinHydrogen    off    ;# don't couple langevin bath to hydrogens


# Output
outputName          $outputname

restartfreq         500     ;# 500steps = every 1ps
dcdfreq             250
outputEnergies      100
outputPressure      100


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

wrapWater     on
wrapNearest   on

# Spherical boundary conditions
#sphericalBC         on
#sphericalBCcenter   30.3081743413, 28.8049907121, 15.353994423
#sphericalBCr1       26.0
#sphericalBCk1       10
#sphericalBCexp1     2

apbsForces       on
apbsPQRFile      ubq.pqr
apbsForcesConfig {
  grid 0.56 0.58 0.5
  recalculateGrid on
  srfm 2
  chgm 1
  bcfl 1
  debug 0
  verbose 1
  pdie 2.0000
  sdie 78.5400
  sdens 10.00
  srad 1.40
  swin 0.30
  temp 298.15
  gamma 0.105
  sp_apbs off
  wpot off
}




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

# Minimization
minimize            100
reinitvels          $temperature

run 2500 ;# 5ps

