# -*- tcl -*- set numsteps 100000 # Set the name of this job set job smd_ree_bp # Input # Physical description paraTypeCharmm on structure step3_charmm2namd.psf # CHARMM36 force field parameters 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_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/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 1-4scaling 1.0 exclude scaled1-4 rigidBonds all useSettle on # Cutoffs and approximations switchdist 10.0 cutoff 12.0 pairlistdist 13.5 stepspercycle 20 timestep 1.0 # Initial data and boundary conditions coordinates step3_charmm2namd.pdb; # One is as good as another set inputname step4_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) COMmotion no zeroMomentum yes seed 12498502 # Thermodynamic ensemble temperature 0.0 langevin on langevinTemp 300.0 langevinDamping 10.0 # Output # Main output and restarts outputName ${job} binaryOutput yes restartName ${job} restartFreq 5000 binaryRestart yes # Trajectory output DCDfile ${job}.dcd DCDfreq 500 DCDUnitCell yes # Standard output frequencies outputEnergies 500 outputMomenta 500 outputTiming 500 # Enable the collective variables module (Colvars) colvars on # Load main Colvars configuration: it can be all contained in this file, # but we are doing it in pieces to control what to load cv configfile multi.colvars.in # Protocol for a 1D SMD simulation (also includes TI PMF calculation) source drag_3d.namd # Execute the MD run run ${numsteps}