#forcefield
paratypecharmm     on
parameters         ../../TOOLS/par_all27_prot_lipid-a.prm

#molecules
structure          all1.psf
coordinates        all1.pdb
bincoordinates      equ3.restart.coor
#binvelocities      equ2.restart.vel
extendedSystem      equ3.xsc 

temperature         310
reassignFreq        100
reassignTemp       25
reassignIncr       25
reassignHold       310

#constraints
constraints        on
consref           equ1-c3n.pdb   # protein_only.coor
conskfile         equ1-c3n.pdb   # protein_cons.pdb
conskcol           B

#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         equ3n
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   76. 0 0
#cellBasisVector2   0 76.5 0
#cellBasisVector3   0 0 76
PMEGridSizeX       80
PMEGridSizeY       80
PMEGridSizeZ       100


#minimize 1000

run 25000