# This is a namd configuration file

## Single QM region with MM water box
structure       ionized.psf
coordinates     YZZ-namd-equil-last-1.pdb


Continuing a job from the restart files
if {1} {
set inputname      YZZ_equil_MM
binCoordinates     $inputname.coor
#binVelocities      $inputname.vel  ;# remove the "temperature" entry if you use this!
extendedSystem     $inputname.xsc
} 





cellBasisVector1 64.945    0       0
cellBasisVector2 0     65.353      0
cellBasisVector3 0     0       67.919
cellOrigin 55.318   57.874   55.561

seed            7910881

# Output Parameters

binaryoutput	no
outputname 	YZZ-QM-min-out
outputenergies 	1
outputtiming 	1
outputpressure 	1
binaryrestart 	yes
dcdfile 	YZZ-QM-min-out.dcd
dcdfreq 	1
XSTFreq 	1
restartfreq 	100
restartname 	YZZ-QM-min-out.restart

# mobile atom selection:

constraints          on
consexp              2
consref              YZZ-restraint.pdb     
conskfile            YZZ-restraint.pdb      
conskcol             B                          
constraintScaling    5.0



#selectConstraints    on

#selectConstrX
#selectConstrY
#selectConstrZ


# PME Parameters

PME 		on
PMEGridspacing 	1


set temperature 300

temperature	$temperature

# Thermostat Parameters

langevin 	    on
langevintemp        $temperature
langevinHydrogen    on
langevindamping     50


# Barostat Parameters

usegrouppressure        yes
useflexiblecell         no
useConstantArea         no
langevinpiston 	        on
langevinpistontarget    1.01325
langevinpistonperiod    200
langevinpistondecay     100
langevinpistontemp      $temperature
surfacetensiontarget    0.0
strainrate              0. 0. 0.


wrapAll         on
wrapWater       on

# Integrator Parameters

timestep 	        0.5
firstTimestep 	        0
fullElectFrequency      1
nonbondedfreq 	        1


# Force Field Parameters

paratypecharmm  on
parameters	../CHARMpars/toppar_all36_carb_glycopeptide.str
parameters      ../CHARMpars/toppar_water_ions_namd.str
parameters	../CHARMpars/toppar_all36_na_nad_ppi_gdp_gtp.str
parameters	../CHARMpars/par_all36_carb.prm
parameters	../CHARMpars/par_all36_cgenff.prm
parameters	../CHARMpars/par_all36_lipid.prm
parameters	../CHARMpars/par_all36_na.prm
parameters 	../CHARMpars/par_all36_prot.prm
parameters      ../common/DMP_ABD769.prm



#printExclusions on
exclude 	scaled1-4
1-4scaling 	1.0
rigidbonds 	none
cutoff 		12.0
pairlistdist 	14.0
switching 	on
switchdist 	10.0

stepspercycle   1


# Truns ON or OFF the QM calculations
qmForces        on

qmParamPDB     "YZZ-namd-QM-0.pdb"

qmColumn        "beta"

qmBondColumn    "occ"

#Link Atoms

qmBondDist           on

#qmLinkElement        



# Number of simultaneous QM simulations per node
QMSimsPerNode   1

QMElecEmbed on


QMSwitching on


QMSwitchingType shift


QMPointChargeScheme none


QMBondScheme "cs"


#qmBaseDir  "/home/xzhfood/mdsim/YZZ-namd/YZZ-QM-MM"

#qmBaseDir  "/dev/shm/YZZ-NAMD_MIN"

# Directory where QM calculations will be ran.
# This should be a fast read/write location, such as a RAM
# folder (/dev/shm on linux distros). You will need to create such folder.
qmBaseDir  "/dev/shm/NAMD_Example1"

# The string passed to "qmConfigLine" will be copied and pasted at the very
# begining of the configuration file for the chosen QM software.
## ORCA
qmConfigLine    "! B3LYP 6-31G Grid4 PAL4 EnGrad TightSCF"
qmConfigLine    "%%output PrintLevel Mini Print\[ P_Mulliken \] 1 Print\[P_AtCharges_M\] 1 end"


#qmConfigLine     "%%pal nprocs 10 end"



# construction of ORCA's input file.
qmMult          "1 2"

qmCharge        "1 -1"

qmSoftware      "orca"

qmExecPath     "/home/xzhfood/software/orca_4_1_2_linux_x86-64_openmpi313/orca"
 
QMOutStride     1
 
QMPositionOutStride     1

# Number of steps in the QM/MM simulation.
minimize  100
run 2000