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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: Annealing.conf,v $
#       $Author: johns $        $Locker:  $             $State: Exp $
#       $Revision: 1.1 $       $Date: 2016/07/13 19:14:19 $
#
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##START HERE###
##Simulation Template##
# Simulation conditions
coordinates wef123_qwikMD.pdb
structure wef123_qwikMD.psf

binCoordinates $inputname.restart.coor
binVelocities $inputname.restart.coor
extendedSystem $inputname.restart.coor

# Simulation conditions
temperature 60


# Harmonic constraints

constraints on
consref qwikmd_equilibration_0_constraints.pdb
conskfile qwikmd_equilibration_0_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


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

# Integrator Parameters

timestep 2
firstTimestep 0
fullElectFrequency 2
nonbondedfreq 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 all


#Implicit Solvent Parameters

gbis                on
alphaCutoff         14.0
ionConcentration    0.15

# Script
set Temp 300
set barostat 1
set nSteps 500
for {set t 60} {$t <= $Temp} {incr t} {run $nSteps;langevintemp $t;if {$barostat} {langevinpistontemp $t}}
