#forcefield
paratypecharmm on
parameters par_all27_prot_lipid.inp

#molecules
structure ions_added.psf
coordinates ions_added.pdb
bincoordinates after_min.restart.coor
#binvelocities a.restart.vel
extendedSystem after_min.xsc

temperature 310
#reassignFreq 100
#reassignTemp 25
#reassignIncr 25
#reassignHold 300

#constraints
constraints on
consref protein_only.coor
conskfile protein_cons.pdb
conskcol X

#temp & pressure coupling
langevin on
langevinTemp 10
langevinDamping 1
#useGroupPressure yes
#useFlexibleCell no
#LangevinPiston on
#LangevinPistonTarget 1
#LangevinPistonPeriod 200
#LangevinPistonDecay 500
#LangevinPistonTemp 10

#output
outputname restr_md
outputEnergies 10
restartfreq 500
DCDfreq 500
binaryoutput no
binaryrestart yes
outputTiming 100
wrapAll on
wrapNearest on

#integrator
timestep 1
nonbondedFreq 1
fullElectFrequency 4
stepspercycle 20

#approximations
rigidBonds all
rigidTolerance 0.00000001
cutoff 12
switching on
switchdist 10
pairlistdist 14
margin 3
exclude scaled1-4
1-4scaling 1.0 # 1.0 for Charmm, 0.833333 for Amber
PME on
#cellBasisVector1 114.39 0 0
#cellBasisVector2 0 120.16 0
#cellBasisVector3 0 0 141.96
PMEGridSizeX 120
PMEGridSizeY 120
PMEGridSizeZ 120


#minimize 1000

run 250000