# Simulation in NPT ensemble 

# Adjustable Parameters
structure          minequ.psf
coordinates        minequ.coor
velocities         minequ.vel 

#output
outputName         res_md
restartfreq        1000  ;#1ps
dcdfreq            1000  ;#1ps
outputEnergies     1000  ;#1ps
binaryoutput       off
#xstFreq            10000  ;#10ps

# force field params
paratypeCharmm  on
parameters      par_all27_prot_lipid_na.inp
exclude         scaled1-4
1-4scaling      1.0
switching       on
switchdist      8.0
cutoff          10.0
pairlistdist    12.0
 
# integrator params
timestep           1.0
rigidBonds         all
nonbondedFreq      1
fullElectFrequency 2
stepspercycle      10

# Periodic boundary conditions
cellBasisVector1    37.0       0.0       0.0
cellBasisVector2     0.0      37.0       0.0
cellBasisVector3     0.0       0.0      36.0
#cellOrigin           6.3301   -3.6934   -2.9505
cellOrigin           0.0       0.0       0.0 
wrapWater            on
wrapAll              on

# constant temperature & pressure coupling

# use lighter damping now that system is equilibrated
langevin          on
langevinDamping   1
langevinTemp      300K
langevinHydrogen  off
useGroupPressure   yes ;#smaller fluctuations
useFlexibleCell    no  
langevinPiston     on 
langevinPistonTarget 1.01325  ;#pressure in bar ->1 atm
langevinPistonPeriod 100      ;#oscillation period around 100fs
langevinPistonDecay   50.     ;#oscillation decay time of 50fs
langevinPistonTemp    300K
   
## EXECUTION SCRIPT
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reinitvels	300K
run           500000    ;#500ps