# NAMD configuration file for PROTEIN_DNA EQUILIBRATION #Initialization firsttimestep 0 # molecular system set output pro_dna_minimization #set input barstar192 #Input files structure pro_dna_ion_wat.psf coordinates pro_dna_ion_wat.pdb #bincoordinates $input.restart.coor #binvelocities $input.restart.vel #extendedSystem $input.restart.xsc #Ouput files outputName $output restartName $output.restart binaryoutput off binaryrestart on #PBC #wrapWater on wrapAll off wrapnearest off #cell information cellbasisvector1 72.0 0. 0. cellbasisvector2 0. 72.0 0. cellbasisvector3 0. 0. 72.0 cellorigin 0.0 0.0 0.0 # force field paraTypeCharmm on parameters par_all27_prot_na.prm exclude scaled1-4 1-4scaling 1.0 cosangle on # approximations #switching off #switchdist 10 cutoff 99 #pairlistdist 13.5 margin 15 #integrator timestep 1.0 #rigidBonds all ;# needed for 2fs steps nonbondedFreq 1 fullElectFrequency 2 stepspercycle 10 #PME (for full-system periodic electrostatics) #PME yes #PMEGridSizeX 64 #PMEGridSizeY 64 #PMEGridSizeZ 64 #output restartfreq 1000 ;# 500steps = every 1ps dcdfreq 1000 xstFreq 1000 outputEnergies 1000 outputtiming 1000 #outputPressure 1000 #protocol #set temperature 300 #temperature $temperature #reassignFreq 1000 #reassigntemp $temperature #reassignIncr 5 #reassignHold 300 #rescalefreq 10 #rescaletemp $temperature # Constant Pressure Control (variable volume) #useGroupPressure yes ;# needed for 2fs steps #useFlexibleCell no ;# no for water box, yes for membrane #useConstantArea no ;# no for water box, yes for membrane #langevinPiston on #langevinPistonTarget 1.01325 ;# in bar -> 1 atm #langevinPistonPeriod 200. #langevinPistonDecay 100. #langevinPistonTemp $temperature # Constant Temperature Control langevin on ;# do langevin dynamics langevinDamping 0.5 ;# damping coefficient (gamma) of 2/ps langevinTemp 300 langevinHydrogen no ;# don't couple langevin bath to hydrogens #Constraints #constraints on #consexp 2 #consref barstar_constraints.pdb #conskfile barstar_constraints.pdb #conskcol B #constraintScaling 1.0 #Minimization #minimization on #minTinyStep 1.0e-6 #minBabyStep 1.0e-2 #minLineGoal 1.0e-4 #script minimize 5000 #run 300000