cwd 		/home/ambrish/modelsimulation/model1/simulation  	# working directory for simulation
seed            1234567

structure 	Model1p_wb_neutral.psf	#  PSF file name 
coordinates 	model1_equilibration.coor	# From equilibration step
velocities	model1_equilibration.vel	# From equilibration step
extendedSystem  model1_equilibration.xsc	# From equilibration step


firsttimestep	142000

#Force field Parameters
paraTypeCharmm	on			#  use CHARMM-type PSF <=> default is XPLOR.
parameters	par_all27_prot_na.prm	# CHARMM parameter file
parameters	toppar_prot_na_all.str	# CHARMM topology file for phosphorylated Serine	


outputEnergies	10
outputTiming	100
xstFreq		100
dcdFreq		100
wrapAll		on
wrapNearest	on

timestep	1
nonBondedFreq	2
fullElectFrequency 4
stepsPerCycle	20

switching	on
switchDist	8.0
cutoff		10.0	
pairlistdist	11.5
# the z dimension is going to shrink so pad sufficiently
# the margin could be reduced once the cell is equilibrated
margin 2

Pme		on
PmeGridsizeX	64
PmeGridsizeY	64
PmeGridsizeZ	54	

exclude		scaled1-4
1-4scaling	1.0

# use lighter damping now that system is equilibrated
langevin		on
langevinDamping		1
langevinTemp		310    ;
langevinHydrogen	no

# use lighter damping now that system is equilibrated
langevinPiston		on
langevinPistonTarget	1.01325
langevinPistonPeriod	200
langevinPistonDecay	500
langevinPistonTemp	310

useGroupPressure	yes	# smaller fluctuations
useFlexibleCell		no	# allow dimensions to fluctuate independently
useConstantRatio	no	# fix shape in x-y plane

binaryoutput	off
outputname	model1_simulation

	
run 10000000