def setup_aatopology(self): GMIN.initialize() pot = GMINPotential(GMIN) coords = pot.getCoords() nrigid = coords.size / 6 print "I have %d water molecules in the system" % nrigid print "The initial energy is", pot.getEnergy(coords) water = tip4p.water() system = RBTopology() system.add_sites([deepcopy(water) for i in xrange(nrigid)]) self.potential = pot self.nrigid = nrigid self.render_scale = 0.3 self.atom_types = system.get_atomtypes() self.draw_bonds = [] for i in xrange(nrigid): self.draw_bonds.append((3 * i, 3 * i + 1)) self.draw_bonds.append((3 * i, 3 * i + 2)) return system
def setup_aatopology(self): GMIN.initialize() pot = GMINPotential(GMIN) coords = pot.getCoords() nrigid = coords.size / 6 print "I have %d water molecules in the system"%nrigid print "The initial energy is", pot.getEnergy(coords) water = create_base() system = RBTopology() system.add_sites([deepcopy(water) for i in xrange(nrigid)]) self.potential = pot self.nrigid = nrigid self.render_scale = 0.15 self.atom_types = system.get_atomtypes() self.draw_bonds = [] for i in xrange(nrigid-1): self.draw_bonds.append((2*i, 2*i+1)) self.draw_bonds.append((2*i, 2*i+2)) return system
def setup_aatopology(self): self.write_coords_data() GMIN.initialize() self.pot = GMINPotential(GMIN) coords = self.pot.getCoords() self.nrigid = coords.size / 6 assert (self.nrigid == self.nmol) #self.nrigid = self.nmol otp = self.make_otp() topology = RBTopology() topology.add_sites([deepcopy(otp) for i in xrange(self.nrigid)]) self.render_scale = 0.2 self.atom_types = topology.get_atomtypes() self.draw_bonds = [] for i in xrange(self.nrigid): self.draw_bonds.append((3 * i, 3 * i + 1)) self.draw_bonds.append((3 * i, 3 * i + 2)) self.params.double_ended_connect.local_connect_params.tsSearchParams.iprint = 10 return topology
def setup_aatopology(self): self.write_coords_data() GMIN.initialize() self.pot = GMINPotential(GMIN) coords = self.pot.getCoords() self.nrigid = coords.size/6 assert(self.nrigid == self.nmol) #self.nrigid = self.nmol otp = self.make_otp() topology = RBTopology() topology.add_sites([deepcopy(otp) for i in xrange(self.nrigid)]) self.render_scale = 0.2 self.atom_types = topology.get_atomtypes() self.draw_bonds = [] for i in xrange(self.nrigid): self.draw_bonds.append((3*i, 3*i+1)) self.draw_bonds.append((3*i, 3*i+2)) self.params.double_ended_connect.local_connect_params.tsSearchParams.iprint = 10 return topology