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'])
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'])
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'])