structure 	grama.psf
coordinates 	equil_out.coor
velocities	equil_out.vel
extendedSystem  equil_out.xsc
parameters	par_all27_prot_lipid.inp 
parameters	par-extraterms.inp 	
paraTypeCharmm	on

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

timestep	1
nonBondedFreq	2
fullElectFrequency 4
stepsPerCycle	20

switching	on
switchDist	8.5
cutoff		10	
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	32
PmeGridsizeY	32
PmeGridsizeZ	64	

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		yes	# allow dimensions to fluctuate independently
useConstantRatio	yes	# fix shape in x-y plane

binaryoutput	off
outputname	nptsim_out

firsttimestep	20000
run 20000