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)