timestep 1.0 structure chainH_final.psf coordinates chainH_final.pdb # Input #paraTypeCharmm on #arameters par_all36_na.prm parameters par_all22_prot_cmap.inp wrapWater on wrapAll on # Force-Field Parameters exclude scaled1-4 1-4scaling 1.0 cutoff 12.0 switching on switchdist 10.0 pairlistdist 14.0 # Integrator Parameters #timestep 1.0 ;# 2fs/step rigidBonds all ;# needed for 2fs steps nonbondedFreq 1 fullElectFrequency 2 stepspercycle 10 # Constant Temperature Control langevin on ;# do langevin dynamics langevinDamping 1 ;# damping coefficient (gamma) of 5/ps #langevinTemp $temperature #langevinHydrogen no ;# don't couple langevin bath to hydrogens #restartfreq 1000 ;# 500steps = every 1ps #dcdfreq 500 #xstFreq 5000 #outputEnergies 100 #outputPressure 100 extraBonds on extraBondsFile restrain_nucleic_all colvars on colvarsConfig US-Z.in