set num_replicas 4 #set temperature 300 set min_temp 300 set max_temp 330 set steps_per_run 1000 set num_runs 500 # num_runs should be divisible by runs_per_frame * frames_per_restart set runs_per_frame 10 set frames_per_restart 5 set namd_config_file "ubq_ww_pcv1.conf" set output_root "output/%s/nucleosome" ; # directories must exist #set pdbRoot "input/start.%d.pdb" #set input_root "input/nucleosome-%d.restart" ; # initial configurations # the following used only by show_replicas.vmd set psf_file "ionized.psf" set initial_pdb_file "charge_mg.pdb" set fit_pdb_file "nuclesome.pdb"