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

# input
coordinates             NSD1-SET-Crystalstructure-original-nowater_autopsf-solvate.pdb
structure               NSD1-SET-Crystalstructure-original-nowater_autopsf-solvate.psf
parameters              D:/Program Files/University of Illinois/VMD/plugins/noarch/tcl/readcharmmpar1.2/par_all27_prot_lipid_na.inp
parameters              C:/Users/Daan/Documents/PhD-KNU/Correct-AdoMet/AdoMet-paper-parameters-auto.par
paratypecharmm          on

# output
set output              NSD1-SET-Crystalstructure-original-nowater_autopsf-solvate-namd
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



# Scripting

minimize            100
reinitvels          $temperature
run                 200