structure Graphene_thy_wat.psf coordinates Graphene_thy_wat.pdb set temp 298.00; set outputname step4_equilibration; # read system values written by CHARMM (need to convert uppercases to lowercases) #exec tr "\[:upper:\]" "\[:lower:\]" < ../step3_pbcsetup.str | sed -e "s/ =//g" > step3_pbcsetup.namd.str source step3_pbcsetup.namd.str temperature $temp; outputName $outputname; # base name for output from this run # NAMD writes two files at the end, final coord and vel # in the format of first-dyn.coor and first-dyn.vel firsttimestep 0; # last step of previous run restartfreq 500; # 500 steps = every 1ps dcdfreq 1000; dcdUnitCell yes; # the file will contain unit cell info in the style of # charmm dcd files. if yes, the dcd files will contain # unit cell information in the style of charmm DCD files. xstFreq 1000; # XSTFreq: control how often the extended systen configuration # will be appended to the XST file outputEnergies 125; # 125 steps = every 0.25ps # The number of timesteps between each energy output of NAMD outputTiming 1000; # The number of timesteps between each timing output shows # time per step and time to completion # Force-Field Parameters paraTypeCharmm on; # We're using charmm type parameter file(s) # multiple definitions may be used but only one file per definition parameters toppar/par_all36m_prot.prm parameters toppar/par_all36_na.prm parameters toppar/par_all36_carb.prm parameters toppar/par_all36_lipid.prm parameters toppar/par_all36_cgenff.prm parameters toppar/toppar_water_ions.str parameters toppar/toppar_dum_noble_gases.str parameters toppar/toppar_all36_prot_d_aminoacids.str parameters toppar/toppar_all36_prot_fluoro_alkanes.str parameters toppar/toppar_all36_prot_heme.str parameters toppar/toppar_all36_prot_na_combined.str parameters toppar/toppar_all36_prot_retinol.str parameters toppar/toppar_all36_na_nad_ppi.str parameters toppar/toppar_all36_na_rna_modified.str parameters toppar/toppar_all36_lipid_bacterial.str parameters toppar/toppar_all36_lipid_cardiolipin.str parameters toppar/toppar_all36_lipid_cholesterol.str parameters toppar/toppar_all36_lipid_inositol.str parameters toppar/toppar_all36_lipid_lps.str parameters toppar/toppar_all36_lipid_miscellaneous.str parameters toppar/toppar_all36_lipid_model.str parameters toppar/toppar_all36_lipid_prot.str parameters toppar/toppar_all36_lipid_sphingo.str parameters toppar/toppar_all36_lipid_yeast.str parameters toppar/toppar_all36_lipid_hmmm.str parameters toppar/toppar_all36_lipid_detergent.str parameters toppar/toppar_all36_carb_glycolipid.str parameters toppar/toppar_all36_carb_glycopeptide.str parameters toppar/toppar_all36_carb_imlab.str # These are specified by CHARMM exclude scaled1-4 # non-bonded exclusion policy to use "none,1-2,1-3,1-4,or scaled1-4" # 1-2: all atoms pairs that are bonded are going to be ignored # 1-3: 3 consecutively bonded are excluded # scaled1-4: include all the 1-3, and modified 1-4 interactions # electrostatic scaled by 1-4scaling factor 1.0 # vdW special 1-4 parameters in charmm parameter file. 1-4scaling 1.0 switching on vdwForceSwitching yes; # New option for force-based switching of vdW # if both switching and vdwForceSwitching are on CHARMM force # switching is used for vdW forces. # You have some freedom choosing the cutoff cutoff 12.0; # may use smaller, maybe 10., with PME switchdist 10.0; # cutoff - 2. # switchdist - where you start to switch # cutoff - where you stop accounting for nonbond interactions. # correspondence in charmm: # (cutnb,ctofnb,ctonnb = pairlistdist,cutoff,switchdist) pairlistdist 14.0; # stores the all the pairs with in the distance it should be larger # than cutoff( + 2.) stepspercycle 20; # 20 redo pairlists every ten steps pairlistsPerCycle 2; # 2 is the default # cycle represents the number of steps between atom reassignments # this means every 20/2=10 steps the pairlist will be updated # Integrator Parameters timestep 2.0; # fs/step rigidBonds all; # Bound constraint all bonds involving H are fixed in length rigidTolerance 0.000001; nonbondedFreq 1; # nonbonded forces every step fullElectFrequency 1; # PME every step # Constant Temperature Control ONLY DURING EQUILB reassignFreq 500; # reassignFreq: use this to reassign velocity every 500 steps reassignTemp $temp; # Periodic Boundary conditions. Need this since for a start... cellBasisVector1 $a 0.0 0.0; # vector to the next image cellBasisVector2 0.0 $b 0.0; cellBasisVector3 0.0 0.0 $c; cellOrigin $xcen $ycen $zcen; # the *center* of the cell wrapWater on; # wrap water to central cell wrapAll on; # wrap other molecules too wrapNearest off; # use for non-rectangular cells (wrap to the nearest image) # PME (for full-system periodic electrostatics) #exec python ../checkfft.py $a $b $c > checkfft.str #source checkfft.str PME yes; PMEInterpOrder 6; # interpolation order (spline order 6 in charmm) PMEGridSizeX 54; # should be close to the cell size PMEGridSizeY 40; # corresponds to the charmm input fftx/y/z PMEGridSizeZ 64; # Pressure and volume control useGroupPressure yes; # use a hydrogen-group based pseudo-molecular viral to calcualte pressure and # has less fluctuation, is needed for rigid bonds (rigidBonds/SHAKE) useFlexibleCell no; # yes for anisotropic system like membrane useConstantRatio no; # keeps the ratio of the unit cell in the x-y plane constant A=B langevin on langevinDamping 1.0 langevinTemp $temp langevinHydrogen off # constant pressure #langevinPiston on #langevinPistonTarget 1.01325 #langevinPistonPeriod 20.0 #langevinPistonDecay 5.0 #langevinPistonTemp $temp #Fixing Atoms fixedAtoms on fixedAtomsFile Graphene_thy_wat_fixed.pdb ;# flags are in this file fixedAtomsCol B ;# set beta non-zero to fix an atom # planar restraint #colvars on #exec sed -e "s/\$bb/1.0/g" -e "s/\$sc/0.1/g" mdsetup_restraint.namd.col > restraints/$outputname.col #colvarsConfig Graphene_ade_water_restraint.namd.col minimize 100000 numsteps 90000000 run 500000