# NAMD configuration file for INSULIN MINIMIZATION and EQUILIBRATION
#Initialization
firsttimestep      0

# output file
set output            xxx_minimize_gromos
outputName            $output
restartName           $output.restart
binaryoutput          no
binaryrestart         no

#PBC
wrapWater           on
wrapAll             on

#cell information
cellbasisvector1  50.000   0.      0.
cellbasisvector2   0.     50.000   0.
cellbasisvector3   0.      0.     50.000

# force field
gromacs               on
grotopfile          topol.top
grocoorfile         xxxxx.gro
exclude             scaled1-4
1-4scaling          1
#vdwGeometricSigma   no
#limitdist           0
#LJcorrection        no

# approximations
switching           off
cutoff              10
pairlistdist        13.5
margin              1

#integrator
timestep            2.0
rigidBonds          all  ;# needed for 2fs steps
rigidTolerance      0.0005
nonbondedFreq       1
fullElectFrequency  2
stepspercycle       10

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

#output
restartfreq         1000     ;# 500steps = every 1ps
dcdfreq             1000
xstFreq             1000
outputEnergies      500
outputPressure      500

#protocol
set temperature      0
temperature          $temperature
#reassignFreq         1000
#reassignIncr         5
#reassignHold         300

# Constant Pressure Control (variable volume)
useGroupPressure      yes ;# needed for 2fs steps
useFlexibleCell       no  ;# no for water box, yes for membrane
useConstantArea       no  ;# no for water box, yes for membrane
langevinPiston        on
langevinPistonTarget  1.01325 ;#  in bar -> 1 atm
langevinPistonPeriod  200.
langevinPistonDecay   100.
langevinPistonTemp    300

#Minimization
minimization        on
minTinyStep         1.0e-6
minBabyStep         1.0e-2
minLineGoal         1.0e-4

#script
minimize 50000