structure       test.psf
coordinates     test.pdb
temperature     0
parameters      par_all27_prot_lipid.inp 
paraTypeCharmm  on

outputEnergies  500
outputTiming    500
xstFreq         500
dcdFreq         500
wrapAll         on
wrapNearest     on

rigidbonds      all
timestep        2
nonBondedFreq   2
fullElectFrequency 4
stepsPerCycle   20
exclude         scaled1-4
1-4scaling      1.0

switching       on
switchDist      8
cutoff          9
pairlistdist    11.5

cellBasisVector1        65.00   00.00   00.00
cellBasisVector2        00.00   70.00   00.00
cellBasisVector3        00.00   00.00   65.00
cellOrigin -6.91  -12.71  -10.24

Pme             on
PmeGridsizeX    70
PmeGridsizeY    75
PmeGridsizeZ    70


fixedAtoms              on
fixedAtomsForces        on
fixedAtomsFile          test_fix_backbone.pdb
fixedAtomsCol           B

constraints     on
consRef         test_restrain_ca.pdb
consKFile       test_restrain_ca.pdb
consKCol        B

langevin                on
langevinDamping         10
langevinTemp            298
langevinHydrogen        no

langevinPiston          on
langevinPistonTarget    1.01325
langevinPistonPeriod    200
langevinPistonDecay     100
langevinPistonTemp      298

useGroupPressure        yes     # smaller fluctuatios

binaryoutput    off
outputname      test_equil

# run one step to get into scripting mode
minimize 0

# turn off until later
langevinPiston  off

# minimize nonbackbone atoms
minimize 1000
output test_min_fix

# min all atoms
fixedAtoms      off
minimize 1000
output test_min_all

# heat with CAs restrained
# langevin      on
run 15000
output test_heat

# equilibrate volume with CAs restrained
langevinPiston  on
run 10000
output test_equil_ca

# equilibrate volume without restraints
constraintScaling       0
run 300000
