# Minimization of 
# 3d optimized in a 20 Water Box

structure         ../common/molcom_wb.psf
coordinates       ../common/molcom_wb.pdb
binCoordinates	../run1vel3/res.coor
binVelocities	../run1vel3/res.vel
extendedSystem	../run1vel3/res.xsc


set temperature    300 
set outputname     molcom
set restartname    res


firsttimestep      0
# Input
paraTypeCharmm	    on
parameters          ../common/par_all27_prot_lipid.inp

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


# Integrator Parameters
timestep            1.0  
rigidBonds          none  
nonbondedFreq       1
fullElectFrequency  2  
stepspercycle       10


# Constant Temperature Control
langevin            on    
langevinDamping     5     
langevinTemp        $temperature
langevinHydrogen    off    


## Periodic Boundary Conditions
cellBasisVector1     57.9     0.     0.
cellBasisVector2      0.     53.7     0.
cellBasisVector3      0.     0.     57.3
cellOrigin           11.2     10.0     6.3
wrapAll             on

# PME (for full-system periodic electrostatics)
PME                 yes
PMEGridSizeX        60
PMEGridSizeY        54
PMEGridSizeZ        60



# Output
outputName          $outputname
restartName         $restartname
outputEnergies      100
outputPressure      100
restartfreq         100     
dcdfreq             100
xstFreq             100



velDCDfile		vel.dcd
velDCDfreq		100





run	4000000