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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: SMD.conf,v $
#       $Author: jribeiro $        $Locker:  $             $State: Exp $
#       $Revision: 1.2 $       $Date: 2017/05/10 19:03:08 $
#
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##START HERE###
##Simulation Template##
# Simulation conditions
# 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 40
outputtiming 40
outputpressure 40
binaryrestart yes
dcdfile qwikmd_equilibration_0.dcd
dcdfreq 1000
XSTFreq 1000
restartfreq 1000
restartname qwikmd_equilibration_0.restart


# Thermostat Parameters
langevin on
langevintemp 60
langevinHydrogen    off
langevindamping 1

# Barostat Parameters

usegrouppressure yes
useflexiblecell no
useConstantArea no
langevinpiston on
langevinpistontarget 1
langevinpistonperiod 200
langevinpistondecay 100
langevinpistontemp 300

# Integrator Parameters

timestep 2
firstTimestep 0
fullElectFrequency 2
nonbondedfreq 1
stepspercycle 10

# 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 all


#Implicit Solvent Parameters

gbis                on
alphaCutoff         14.0
ionConcentration    0.15


# Script


# steered dynamics
SMD on
SMDFile $smdFile
SMDk 7.0
SMDVel $pullSpeed
SMDDir 0.0 0.0 1.0
SMDOutputFreq 20

run 5000
