structure ../step5_assembly.xplor_ext.psf coordinates ../step5_assembly.namd.pdb set temp 303.15; outputName step7.1_production; # 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 set inputname step6.6_equilibration; binCoordinates $inputname.coor; # coordinates from last run (binary) binVelocities $inputname.vel; # velocities from last run (binary) extendedSystem $inputname.xsc; # cell dimensions from last run (binary) 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 500; # XSTFreq: control how often the extended systen configuration # will be appended to the XST file outputEnergies 500; # 500 steps = every 1.00ps, #ND: original value is 125 # The number of timesteps between each energy output of NAMD outputTiming 500; # 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_all36_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_all36_prot_retinol.str parameters toppar/toppar_all36_carb_glycopeptide.str parameters toppar/toppar_all36_prot_fluoro_alkanes.str parameters toppar/toppar_all36_prot_na_combined.str parameters toppar/toppar_all36_lipid_bacterial.str parameters toppar/toppar_all36_lipid_miscellaneous.str parameters toppar/toppar_all36_lipid_cholesterol.str parameters toppar/toppar_all36_lipid_yeast.str parameters toppar/toppar_all36_lipid_sphingo.str parameters toppar/toppar_all36_lipid_glycolipid.str parameters toppar/toppar_all36_lipid_inositol.str parameters toppar/toppar_all36_lipid_cardiolipin.str parameters toppar/toppar_all36_lipid_llo.str parameters toppar/toppar_water_ions.str parameters toppar/toppar_dum_noble_gases.str parameters toppar/toppar_all36_na_nad_ppi.str parameters toppar/toppar_all36_carb_chemmod.str source step5_assembly.namd.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 16.0; # 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 nonbondedFreq 1; # nonbonded forces every step fullElectFrequency 1; # PME every step wrapWater on; # wrap water to central cell wrapAll on; # wrap other molecules too if { $boxtype == "hexa" } { wrapNearest on; # use for non-rectangular cells (wrap to the nearest image) } else { wrapNearest off; # use for non-rectangular cells (wrap to the nearest image) } # PME (for full-system periodic electrostatics) source checkfft.str PME yes; PMEInterpOrder 6; # interpolation order (spline order 6 in charmm) PMEGridSizeX $fftx; # should be close to the cell size PMEGridSizeY $ffty; # corresponds to the charmm input fftx/y/z PMEGridSizeZ $fftz; # Constant Pressure Control (variable volume) 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 yes; # yes for anisotropic system like membrane useConstantRatio yes; # keeps the ratio of the unit cell in the x-y plane constant A=B langevinPiston on; # Nose-Hoover Langevin piston pressure control langevinPistonTarget 1.01325; # target pressure in bar 1atm = 1.01325bar langevinPistonPeriod 50.0; # oscillation period in fs. correspond to pgamma T=50fs=0.05ps # f=1/T=20.0(pgamma) langevinPistonDecay 25.0; # oscillation decay time. smaller value correspons to larger random # forces and increased coupling to the Langevin temp bath. # Equall or smaller than piston period langevinPistonTemp $temp; # coupled to heat bath # Constant Temperature Control langevin on; # langevin dynamics langevinDamping 1.0; # damping coefficient of 1/ps (keep low) langevinTemp $temp; # random noise at this level langevinHydrogen off; # don't couple bath to hydrogens # run numsteps 2500000; # run stops when this step is reached run 2500000; # 5ns