2 """This script shows how to simulate an atomic system with MD,
3 with a secondary structure elastic network to speed things up.
19 st1 = s.create_state()
23 gcp2 = st1.create_molecule(
"GCP2",sequence=seqs[
"GCP2_YEAST"],chain_id=
'A')
30 gcp2.add_representation(a1,resolutions=[0])
31 print(
'building molecule')
35 print(
'adding restraints')
42 for sse
in sses[
'helix']+sses[
'beta']:
54 md_ps = dof.setup_md(gcp2)
57 crosslink_restraints = all_rs,
58 molecular_dynamics_sample_objects=md_ps,
59 molecular_dynamics_steps=5,
60 number_of_best_scoring_models=0,
62 global_output_directory=
'atomistic_output/')