# NAMD CONFIGURATION FILE FOR ER-GRE BENCHMARK # molecular system structure er-gre.psf coordinates er-gre.pdb # force field parameters pro_residues.par parameters nuc_residues.par parameters water+ions.par parameters par22.zinc exclude scaled1-4 1-4scaling 0.4 # approximations switching on switchdist 8 cutoff 12 pairlistdist 13.5 margin 0 stepspercycle 10 # integrator timestep 1.0 # extra forces sphericalBC on sphericalBCcenter 0.0,0.0,0.0 sphericalBCr1 48 sphericalBCk1 10 sphericalBCexp1 2 # output outputenergies 1 outputtiming 50 outputname /tmp/er-gre.out # protocol seed 83623 temperature 300 numsteps 500