def write_ic_fluct_inp(f_out, host, type_na, time_label, cutoff, rootfolder): inp = charmm_fluct.Script(f_out) inp.write_bomlev() inp.initialize_variables(rootfolder, host, type_na, time_label) inp.read_rtf(cutoff) inp.read_seq() inp.read_crd() inp.stream_str(cutoff) inp.read_traj() inp.icfluct() inp.write_icfluct(cutoff) inp.end()
def write_nmainit_inp(f_out, host, type_na, cutoff, rootfolder, scratchfolder): inp = charmm_fluct.Script(f_out) inp.write_bomlev() inp.initialize_variables_nma(rootfolder, scratchfolder, host, type_na, cutoff) inp.read_rtf(cutoff) inp.read_prm() inp.read_seq() inp.read_crd_nma() inp.set_mass_1() inp.minimization() inp.stream_str_nma() inp.nma() inp.end()
def write_ic_avg_inp(f_out, host, type_na, cutoff, rootfolder, distance_average=False): inp = charmm_fluct.Script(f_out) inp.write_bomlev() inp.initialize_variables(rootfolder, host, type_na) inp.read_rtf(cutoff) inp.read_seq() inp.read_crd() inp.stream_str(cutoff) inp.read_traj() inp.icavg(distance_average=distance_average) inp.write_icavg(cutoff) inp.end()