structure ../step2_drude.psf coordinates ../step2_drude.pdb set temp 298; set outputname step4_equilibration; 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 5000; # 2000 steps with 0.5 fs timestep = every 1ps dcdfreq 5000; # 2000 steps with 0.5 fs timestep = every 1ps 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 250; # 250 steps = every 0.25ps # The number of timesteps between each energy output of NAMD outputTiming 5000; # 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_drude/toppar_drude_master_protein_2019g.str; parameters ../toppar_drude/toppar_drude_lipid_2017c.str; parameters ../toppar_drude/toppar_drude_model_2019g.str; parameters ../toppar_drude/toppar_drude_carbohydrate_2019a.str; parameters ../toppar_drude/toppar_drude_nucleic_acid_2017c.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 no; # force-based switching of vdW should not be used for Drude FF mergeCrossterms on # 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) LJcorrection yes 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 0.5; # fs/step. If experiencing instability, try smaller value, e.g., 0.75 or 0.5. # If drudeHardwall is not applicable, please set 0.5. rigidBonds all; # Bound constraint all bonds involving H are fixed in length nonbondedFreq 1; # nonbonded forces every step fullElectFrequency 1; # PME every step # Use Drude polarizable model drude on drudeTemp 1 drudeHardwall on; # Only available in latest NAMD (newer than 2.09). Please comment out this line in old namd. drudeDamping 20.0 drudeBondLen 0.2; # Please set 0.20 if drudeHardwall is not applicable. drudeBondConst 40000 drudeNbtholeCut 5.0 # read system values written by CHARMM (need to convert uppercases to lowercases) #exec tr "\[:upper:\]" "\[:lower:\]" < ../step2_drude.str | sed -e "s/ =//g" > step2_drude.str source ../step2_drude.str; # 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 0.0 0.0 $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) 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 no; # yes for anisotropic system like membrane langevin on langevinDamping 5 langevinTemp $temp langevinHydrogen off # constant pressure langevinPiston on langevinPistonTarget 1.01325 langevinPistonPeriod 50.0 langevinPistonDecay 25.0 langevinPistonTemp $temp # restrints on heavy atoms for minimization and equilibration colvars on colvarsConfig step4_equilibration.col minimize 200 run 200000