cutoff 12.0
pairlistdist 14.0
switching on
switchdist 10.0
PME on
PMEGridspacing 1
wrapAll on
wrapWater on
useConstantRatio yes
parameters Retinal_schiff_based_qwikmd.str
############################################################################
#cr
#cr            (C) Copyright 1995-2009 The Board of Trustees of the
#cr                        University of Illinois
#cr                         All Rights Reserved
#cr
############################################################################


############################################################################
# RCS INFORMATION:
#
#       $RCSfile: MD.conf,v $
#       $Author: jribeiro $        $Locker:  $             $State: Exp $
#       $Revision: 1.2 $       $Date: 2016/02/10 20:41:44 $
#
############################################################################
##START HERE###
##Simulation Template##
# Simulation conditions
coordinates 1qhj_membrane_QwikMD.pdb
structure 1qhj_membrane_QwikMD.psf


binCoordinates MD.restart.coor
binVelocities MD.restart.vel
extendedSystem MD.restart.xsc


# Simulation conditions
#temperature 0




# Harmonic constraints


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




# Output Parameters


binaryoutput no
outputname MD.1
outputenergies 200
outputtiming 200
outputpressure 200
binaryrestart yes
dcdfile MD.1.dcd
dcdfreq 100000
XSTFreq 100000
restartfreq 100000
restartname MD.1.restart




# Thermostat Parameters
langevin on
langevintemp 300
langevinHydrogen    off
langevindamping 1


# Barostat Parameters


usegrouppressure yes
useflexiblecell yes
useConstantArea no
langevinpiston on
langevinpistontarget 1.01325
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 off
alphaCutoff         14.0
ionConcentration    0.15




# Script


run 5000000








set file [open MD.1.check w+]
set done 1
if {[file exists MD.1.restart.coor] != 1 || [file exists MD.1.restart.vel] != 1 || [file exists MD.1.restart.xsc] != 1 } {
	 set do 0
}
if {$done == 1} {
	puts $file "DONE"
    flush $file
  close $file
} else {
	puts $file "One or more files filed to be written"
   flush $file
  close $file
}