2 """This script shows how to simulate an atomic system with MD,
3 with a secondary structure elastic network to speed things up.
6 from __future__
import print_function
19 print(
"This example is too slow to test in debug mode - run without")
20 print(
"internal tests enabled, or without the --run-quick-test flag")
26 st1 = s.create_state()
30 gcp2 = st1.create_molecule(
"GCP2",sequence=seqs[
"GCP2_YEAST"],chain_id=
'A')
37 gcp2.add_representation(a1,resolutions=[0])
38 print(
'building molecule')
42 print(
'adding restraints')
48 name_map={
'A':
'GCP2'})
50 for sse
in sses[
'helix']+sses[
'beta']:
62 md_ps = dof.setup_md(gcp2)
65 crosslink_restraints = all_rs,
66 molecular_dynamics_sample_objects=md_ps,
67 molecular_dynamics_steps=5,
68 number_of_best_scoring_models=0,
70 global_output_directory=
'atomistic_output/')