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

# input
coordinates             /home/a1222834/TRIF_NTD/trif_ionized.pdb
structure               /home/a1222834/TRIF_NTD/trif_ionized.psf
parameters              /home/a1222834/TRIF_NTD/par_all27_prot_lipid.inp
paratypecharmm          on

# output
set output              trif_ionized_min_dynamic
outputname              $output
dcdfile                 ${output}.dcd
xstFile                 ${output}.xst
dcdfreq                 50
xstFreq                 50

binaryoutput            no
binaryrestart           no
outputEnergies          100
restartfreq             1000

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

set temperature         298
temperature             $temperature;  # initial temperature

# Langevin Dynamics
langevin                on;            # do langevin dynamics
langevinDamping         1;              # damping coefficient (gamma) of 1/ps
langevinTemp            $temperature;   # bath temperature
langevinHydrogen        no;             # don't couple langevin bath to hydrogens
seed                    12345


# PBC
cellBasisVector1        49.45 0.00 0.00
cellBasisVector2        0.00 65.58 0.00
cellBasisVector3        0.00 0.00 61.62
cellOrigin              -0.35 -0.91 -1.92
wrapAll                 on
dcdUnitCell             yes


# Scripting

minimize            1000
reinitvels          $temperature
run                 10000000