def test_rip(params):
util.goto_dir(params['sim_dir'])
print "> Pulse with RIP residue rotation"
util.goto_dir('rip')
simulate.pulse(
params['ff'], '../md_merge/md', 'md', 2000,
force.make_rip_fn(params['i_residue'], 300), 100)
def test_puff(params):
util.goto_dir(params['sim_dir'])
util.goto_dir('puff')
print "> Pulse with terminii push"
md = '../md_merge/md'
n = get_n_protein_residues_from_restart(md)
# make push function
pulse_fn = force.make_puff_fn(
[0, 1, 2], [n-3, n-2, n-1], 10.0, 0.1, 300)
simulate.pulse(params['ff'], md, 'md', 2000, pulse_fn, 100)
def test_puff(params):
util.goto_dir(params['sim_dir'])
util.goto_dir('puff')
print "> Pulse with terminii push"
md = '../md_merge/md'
n = get_n_protein_residues_from_restart(md)
# make push function
pulse_fn = force.make_puff_fn([0, 1, 2], [n - 3, n - 2, n - 1], 10.0, 0.1,
300)
simulate.pulse(params['ff'], md, 'md', 2000, pulse_fn, 100)
def test_user_defined_pulse(params):
util.goto_dir(params['sim_dir'])
util.goto_dir('user_pulse')
i, j = params['i_loop_start'], params['i_loop_end']
rotate_loop = RotateLoop(i, j, 0.7)
print "> make restraint_pdb"
restraint_pdb = os.path.abspath('md.restraint.pdb')
in_md = '../md_merge/md'
n = get_n_protein_residues_from_restart(in_md)
residue_indices = range(0, i) + range(j, n)
make_restraint_pdb(in_md, residue_indices, restraint_pdb)
pulse_fn = lambda soup: rotate_loop.apply(soup)
print "> Pulse with user-defined pulse_fn"
simulate.pulse(
params['ff'], '../md_merge/md', 'md', 5000, pulse_fn, 100,
restraint_pdb=restraint_pdb)
def test_user_defined_pulse(params):
util.goto_dir(params['sim_dir'])
util.goto_dir('user_pulse')
i, j = params['i_loop_start'], params['i_loop_end']
rotate_loop = RotateLoop(i, j, 0.7)
print "> make restraint_pdb"
restraint_pdb = os.path.abspath('md.restraint.pdb')
in_md = '../md_merge/md'
n = get_n_protein_residues_from_restart(in_md)
residue_indices = range(0, i) + range(j, n)
make_restraint_pdb(in_md, residue_indices, restraint_pdb)
pulse_fn = lambda soup: rotate_loop.apply(soup)
print "> Pulse with user-defined pulse_fn"
simulate.pulse(params['ff'],
'../md_merge/md',
'md',
5000,
pulse_fn,
100,
restraint_pdb=restraint_pdb)
def test_rip(params):
util.goto_dir(params['sim_dir'])
print "> Pulse with RIP residue rotation"
util.goto_dir('rip')
simulate.pulse(params['ff'], '../md_merge/md', 'md', 2000,
force.make_rip_fn(params['i_residue'], 300), 100)
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'])
