structure step3_input.psf coordinates step3_input.pdb set temp 303.15 set inputname step5_production; 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) # temperature $temp outputname "output/eq_colvars_tcl" dcdfreq 50000; 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 10000; # XSTFreq: control how often the extended systen configuration # will be appended to the XST file outputEnergies 10000; # 5000 steps = every 10ps # The number of timesteps between each energy output of NAMD outputTiming 10000; # The number of timesteps between each timing output shows # time per step and time to completion restartfreq 10000; # 5000 steps = every 10ps # 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/par_interface.prm parameters toppar/toppar_all36_moreions.str parameters toppar/toppar_all36_nano_lig.str parameters toppar/toppar_all36_nano_lig_patch.str parameters toppar/toppar_all36_synthetic_polymer.str parameters toppar/toppar_all36_synthetic_polymer_patch.str parameters toppar/toppar_all36_polymer_solvent.str parameters toppar/toppar_water_ions.str parameters toppar/toppar_dum_noble_gases.str parameters toppar/toppar_ions_won.str parameters toppar/cam.str parameters toppar/toppar_all36_prot_arg0.str parameters toppar/toppar_all36_prot_c36m_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_prot_model.str parameters toppar/toppar_all36_prot_modify_res.str parameters toppar/toppar_all36_na_nad_ppi.str parameters toppar/toppar_all36_na_rna_modified.str parameters toppar/toppar_all36_lipid_sphingo.str parameters toppar/toppar_all36_lipid_archaeal.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_dag.str parameters toppar/toppar_all36_lipid_inositol.str parameters toppar/toppar_all36_lipid_lnp.str parameters toppar/toppar_all36_lipid_lps.str parameters toppar/toppar_all36_lipid_mycobacterial.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_tag.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_lipid_ether.str parameters toppar/toppar_all36_lipid_oxidized.str parameters toppar/toppar_all36_carb_glycolipid.str parameters toppar/toppar_all36_carb_glycopeptide.str parameters toppar/toppar_all36_carb_imlab.str parameters toppar/toppar_all36_label_spin.str parameters toppar/toppar_all36_label_fluorophore.str # Nonbonded Parameters 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 on; # 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 2; # PME every two steps wrapWater on; # wrap water to central cell wrapAll on; # wrap other molecules too # PME (for full-system periodic electrostatics) PME yes; PMEInterpOrder 6; # interpolation order (spline order 6 in charmm) PMEGridSpacing 1.0; # maximum PME grid space / used to calculate grid size # 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 no; # yes for anisotropic system like membrane useConstantRatio no; # keeps the ratio of the unit cell in the x-y plane constant A=B # 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 # Constant pressure 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 corresponds to larger random # forces and increased coupling to the Langevin temp bath. # Equal or smaller than piston period langevinPistonTemp $temp; # coupled to heat bath CUDASOAIntegrate on colvars on colvarsConfig pucker_tcl.colvars source pucker.tcl numsteps 100000