Exemple #1
0
def test_basic_md_merge(params):
    util.goto_dir(params['sim_dir'])

    print "> Fixed-temp1"
    util.goto_dir('md1')
    simulate.langevin_thermometer(params['ff'], '../min/min', 1000, 300, 'md',
                                  10)

    print "> Fixed-temp2"
    util.goto_dir('../md2')
    simulate.langevin_thermometer(params['ff'], '../md1/md', 1000, 300, 'md',
                                  10)

    print "> Merge temp1-temp2"
    util.goto_dir('../md_merge')
    simulate.merge_trajectories(params['ff'], 'md', ['../md1/md', '../md2/md'])
Exemple #2
0
def test_basic_md_merge(params):
  util.goto_dir(params['sim_dir'])

  print "> Fixed-temp1"
  util.goto_dir('md1')
  simulate.langevin_thermometer(
      params['ff'], '../min/min', 1000, 300, 'md', 10)

  print "> Fixed-temp2"
  util.goto_dir('../md2')
  simulate.langevin_thermometer(
      params['ff'], '../md1/md', 1000, 300, 'md', 10)

  print "> Merge temp1-temp2"
  util.goto_dir('../md_merge')
  simulate.merge_trajectories(
      params['ff'], 'md', ['../md1/md', '../md2/md'])
Exemple #3
0
simulate.langevin_thermometer(
    ff, 'minwater', 5000, 300, 'heatwater',  50, 
    restraint_pdb='restrain_protein.pdb')

# cool water back down 10K, hold protein fixed
simulate.langevin_thermometer(
    ff, 'heatwater', 5000, 10, 'coolwater',  50, 
    restraint_pdb='restrain_protein.pdb')

# equilibrate entire system to 10K 
simulate.langevin_thermometer(
    ff, 'coolwater', 5000, 10, 'heat',  50)

# let the system relax without thermometer
simulate.constant_energy(
    ff, 'heat', 5000, 'const',  50)

# then reequilibrate to 10K
simulate.langevin_thermometer(
    ff, 'const', 5000, 10, 'reheat',  50)

# we are ready to apply RIP
pulse_fn = force.make_rip_fn(i_residue, 100)
simulate.pulse(
    ff, 'reheat', 'rip', 5000, pulse_fn, 100)

# combine all sims into one long trajectory for viewing
simulate.merge_trajectories(
    ff, 'equil', ['heatwater', 'coolwater', 'heat', 
                  'const', 'reheat', 'rip'])