def test_restraint(params):
print "> Equil with restraints on "
util.goto_dir(params['sim_dir'])
util.goto_dir('restraint')
in_md = '../md_merge/md'
restraint_pdb = os.path.abspath('md.restraint.pdb')
make_restraint_pdb(
in_md, [params['i_residue']], restraint_pdb, is_backbone_only=False)
simulate.langevin_thermometer(
params['ff'], in_md, 1000, 300, 'md', 10,
restraint_pdb=restraint_pdb)
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_restraint(params):
print "> Equil with restraints on "
util.goto_dir(params['sim_dir'])
util.goto_dir('restraint')
in_md = '../md_merge/md'
restraint_pdb = os.path.abspath('md.restraint.pdb')
make_restraint_pdb(in_md, [params['i_residue']],
restraint_pdb,
is_backbone_only=False)
simulate.langevin_thermometer(params['ff'],
in_md,
1000,
300,
'md',
10,
restraint_pdb=restraint_pdb)
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'])
clean_pdb = '2evq.clean.pdb'
pdbtext.clean_pdb(pdb_code+'.pdb', clean_pdb)
# Generate restart files from PDB
simulate.pdb_to_top_and_crds(ff, clean_pdb, 'sim')
# Make a protein positional restrain_protein.pdb file
make_protein_restraint_pdb('sim', 'restrain_protein.pdb')
# minimize system (mostly water) with protein positions fixed
simulate.minimize(
ff, 'sim', 'minwater', restraint_pdb='restrain_protein.pdb')
# heat only water to 300K, hold protein fixed
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)