# NAMD Config file - autogenerated by NAMDgui plugin
# Author: Jan Saam,  saam@charite.de

# input
coordinates             ionized_Mg.pdb
structure               ionized_Mg.psf
parameters              Par_all27_prot_na.prm
paratypecharmm          on

# output
set output              ionized_MG
outputname              $output
dcdfile                 ${output}.dcd
xstFile                 ${output}.xst
dcdfreq                 5000
xstFreq                 5000

binaryoutput            no
binaryrestart           no
outputEnergies          200
restartfreq             1000
outputPressure          200

fixedAtoms              off

# Basic dynamics
exclude                 scaled1-4
1-4scaling              1
COMmotion               no
dielectric              1.0

# Simulation space partitioning
switching               on
switchdist              9
cutoff                  10
pairlistdist            12

# Multiple timestepping
firsttimestep           0
timestep                1
stepspercycle           20
nonbondedFreq           2
fullElectFrequency      4

# Temperature control

temperature 		20
reassignFreq            500
reassignIncr		25
reassignHold		310

#berendsenPressure                  on
#berendsenPressureTarget            1.01325   # atmospheric pressure
#berendsenPressureCompressibility   4.57e-5   # liquid water
#berendsenPressureRelaxationTime    100.0
#berendsenPressureFreq              10

#langevinPiston        on
#langevinPistonTarget  1.01325      ;# pressure in bar -> 1 atm
#langevinPistonPeriod  100.         ;# oscillation period around 100 fs
#langevinPistonDecay   50.          ;# oscillation decay time of 50 fs
#langevinPistonTemp    310 ;# coupled to heat bath

# Langevin Dynamics
langevin                on;            # do langevin dynamics
langevinDamping         1;              # damping coefficient (gamma) of 1/ps
langevinTemp            310K;   # bath temperature
langevinHydrogen        no;             # don't couple langevin bath to hydrogens
seed                    16345

IMDon    yes
IMDport  2030
IMDfreq  200
IMDwait  off

# Scripting

minimize            5000
reinitvels          310
run                 100000000