# NAMD configuration file
# input
coordinates             7BuY.pdb
structure               7BuY.psf
# molecular system
# output
set output              C:/Users/Belachew/Desktop/7bay/Mpro
outputname              $output
dcdfile                 ${output}.dcd
xstFile                 ${output}.xst
dcdfreq                 50
xstFreq                 50

binaryoutput            no
binaryrestart           no
outputEnergies          100
restartfreq             1000

fixedAtoms              on

# force field
paratypecharmm	on
parameters	par_all36_prot.prm
exclude		scaled1-4
1-4scaling	1.0

# approximations
switching	on
switchdist	8
cutoff		12
pairlistdist	10.5
margin		0
stepspercycle	20
# Basic dynamics
exclude                 scaled1-4
1-4scaling              1
COMmotion               no
dielectric              1.0
# Simulation space partitioning
switching               on
switchdist              9
cutoff                  10
pairlistdist            12
#integrator
timestep 2.0
#output
outputenergies	10
outputtiming	100
binaryoutput	yes

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

# Temperature control

set temperature         310
temperature             $temperature;  # initial temperature
# PBC
cellBasisVector1        51.265 0.00 0.00
cellBasisVector2        0.00 66.171 0.00
cellBasisVector3        0.00 0.00 17.854
cellOrigin              -51.6325 66.171 17.854
wrapAll                 on
dcdUnitCell             yes

PME                     yes
PMEGridSizeX            50
PMEGridSizeY            64
PMEGridSizeZ            16
#scripting
minimize            1000
reinitvels          $temperature
run                 700000