structure step5_charmm2namd.psf coordinates step5_charmm2namd.pdb set temp 303.15; set outputname step6.1_equilibration; # read system values written by CHARMM (need to convert uppercases to lowercases) exec tr "\[:upper:\]" "\[:lower:\]" < ../step5_assembly.str | sed -e "s/ =//g" > step5_charmm2namd.str source step5_charmm2namd.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 1000; # 1000 steps = every 2ps dcdfreq 5000; 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 5000; # 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/par_interface.prm parameters toppar/toppar_all36_nano_lig.str parameters toppar/toppar_all36_nanolig_patch.str parameters toppar/toppar_water_ions.str parameters toppar/toppar_dum_noble_gases.str parameters toppar/toppar_ions_won.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_modify_res.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_lipid_ether.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 parameters toppar/toppar_all36_lipid_cationpi_wyf.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 1.0; # 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 # 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... if { $boxtype == "hexa" } { set b [expr {$a / 2 * sqrt(3)}] set d [expr {$a / 2}] set wrapnearst on } else { set wrapnearst off set d 0.0 } cellBasisVector1 $a 0.0 0.0; # vector to the next image cellBasisVector2 $d $b 0.0; cellBasisVector3 0.0 0.0 $c; cellOrigin 0.0 0.0 $zcen; # the *center* of the cell wrapWater on; # wrap water to central cell wrapAll on; # wrap other molecules too wrapNearest $wrapnearst; # use for non-rectangular cells (wrap to the nearest image) # 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 # 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 yes; # yes for anisotropic system like membrane useConstantRatio yes; # keeps the ratio of the unit cell in the x-y plane constant A=B langevin on langevinDamping 1.0 langevinTemp $temp langevinHydrogen off constraints on consexp 2 consref restraints/prot_posres.ref conskfile restraints/prot_posres.ref conskcol B constraintScaling 10.0 # planar restraint exec sed -e "s/Constant \$fc/Constant 5/g" step5_charmm2namd.colvar.str > restraints/$outputname.col exec sed -e "s/\$tailforce/ 2.5/" -e "s/\$dcleforce/ 2.5/" membrane_hmmm_restraint.namd.col >> restraints/$outputname.col exec sed -e "s/\$tailforce/0.05/" membrane_hmmmc21c31_restraint.namd.col >> restraints/$outputname.col colvars on colvarsConfig restraints/$outputname.col tclBC on tclBCScript { source restraints/water.cons.tcl } tclBCArgs {11 2.5} # dihedral restraint exec sed -e "s/\$FC/500/g" restraints/dihe.txt > restraints/$outputname.dihe extraBonds yes extraBondsFile restraints/$outputname.dihe minimize 10000 numsteps 50000 run 50000