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#cr
#cr            (C) Copyright 1995-2009 The Board of Trustees of the
#cr                        University of Illinois
#cr                         All Rights Reserved
#cr
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# RCS INFORMATION:
#
#       $RCSfile: QMMM-Equi.conf,v $
#       $Author: jribeiro $        $Locker:  $             $State: Exp $
#       $Revision: 1.2 $       $Date: 2017/06/29 20:35:19 $
#
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##START HERE###
##Simulation Template##
# Simulation conditions
coordinates qwikmdTemp.pdb
structure qwikmdTemp.psf

binCoordinates qwikmdTemp.restart.coor
binVelocities qwikmdTemp.restart.coor
extendedSystem qwikmdTemp.restart.coor

# Simulation conditions
temperature 0


# Harmonic constraints

constraints on
consref qwikmdTemp_constraints.pdb
conskfile qwikmdTemp_constraints.pdb
constraintScaling 2
consexp 2
conskcol B


# Output Parameters

binaryoutput no
outputname qwikmd_equilibration_0
outputenergies 1
outputtiming 1
outputpressure 1
binaryrestart yes
dcdfile qwikmd_equilibration_0.dcd
dcdfreq 1
XSTFreq 1
restartfreq 1
restartname qwikmd_equilibration_0.restart


# Thermostat Parameters
langevin on
langevintemp 60
langevinHydrogen    on
langevindamping 50

# Barostat Parameters

usegrouppressure yes
useflexiblecell no
useConstantArea no
langevinpiston on
langevinpistontarget 1
langevinpistonperiod 200
langevinpistondecay 100
langevinpistontemp 60

# Integrator Parameters

timestep 0.5
firstTimestep 0
fullElectFrequency 1
nonbondedfreq 1
stepspercycle   1

# Force Field Parameters

paratypecharmm on
parameters toppar_water_ions_namd.str
parameters toppar_all36_carb_glycopeptide.str
parameters par_all36_lipid.prm
parameters par_all36_na.prm
parameters par_all36_prot.prm
parameters par_all36_carb.prm
parameters par_all36_cgenff.prm
exclude scaled1-4
1-4scaling 1.0
rigidbonds none


#Implicit Solvent Parameters

gbis                on
alphaCutoff         14.0
ionConcentration    0.15

# Truns ON or OFF the QM calculations

qmForces on

#printExclusions on

# Name of a secondary PDB file where the OCCupancy
# or BETA column has the indications for QM or MM atoms.

qmParamPDB     "duoMasto/mastoparan.pdb"

# Indicates qhich column has the QM/MM field.

qmColumn        "beta"

# Number of simultaneous QM simulations per node

QMSimsPerNode   1

# Indicates qhich column has the QM-MM bond information.

qmBondColumn    "occ"

# Indicates wether the value in the BondColumn will define the distance
# between the QM atom and the Dummy atom that will replace the MM atom

# qmBondDist      on

# Indicates if the values in the bond column represent either: 
# LEN: the length betwen the QM and dummy atoms.

# QMBondValueType len

# User defined Link Atom element.

#QMLinkElement "18 38 Cl"

# Indicates what will be the treatment given to QM-MM bonds in terms of
# charge distribution and dummy atom creation and placement.

QMBondScheme "CS"

# This will scale down the point charges representing the classical system 
# as to replicate the switching procedure that NAMD applies to all charged
# interaction.

QMSwitching off

# This option is used to decide which kind of function will be used to scale
# down point charges sent to QM calculations.

QMSwitchingType switch

# This will alter the point charges presented to the QM system.

QMPointChargeScheme zero

# Directory where QM calculations will be ran.

qmBaseDir  "/dev/shm/NAMD.TEST1"

# Indicates to NAMD that ALL forces form NAMD will be ignored and only
# the gradients from the QM software will be applied on the atoms.

qmReplaceAll    OFF

# The QM code will change all QM atom's VdW types to "q"+element for VdW interactions.

QMVdWParams off

# Indicates that no Poitn Charges should be selected and applied in 
# QM systems.

qmElecEmbed     off

# Sets a stride for new point charge determination.

QMPCStride      1

# Indicates that one or more files will be provided with a custom selection
# of point charges.

QMCustomPCSelection     off

# The file will have, in the "qmColumn", the same QM ID provided for a single QM group.

QMCustomPCFile  input-CustomPC-1.0.pdb


# With Live Solvent Selection, NAMD will automatically keep track of the 
# solvent molecules for all QM Groups, and will exchange classical solvent
# molecules with QM solvent molecules every "QMLSSFreq" steps.

QMLiveSolventSel  off

# This indicate which residue type will be used in LSS.

QMLSSResname      TIP3

# Frequency of LSS.

QMLSSFreq         50

# For LSS, this indicates how solvent molecules are selected.

QMLSSMode       dist


# This will indicate which residues are to be used in the determination of the 
# COM of non-solvent QM atoms.

QMLSSRef        "1 RP1 9"

# The string passed to "qmConfigLine" will be copied and pasted at the very
# begining of the configuration file for the chosen QM software.

qmConfigLine    "! B3LYP 6-31G* Grid4 PAL8"

# Multiplicity of the QM region. 

qmMult          "1 1"

# Indicates the charge of each QM region.

qmCharge        "1 0"


# Indicates which QM software should be used.

qmSoftware      "orca"

# Path to the executable

qmExecPath     "/home/user/software/orca/orca"

# Charge mode expected from the QM software. 

QMChargeMode mulliken

# Frequency of QM charge output.

QMOutStride     1

# Frequency of QM ONLY position output.

QMPositionOutStride     1

# Number of steps in the QM/MM simulation

# Script
run 5000
