OrderParameter module

calculation of order parameters of lipid bilayers from a MD trajectory

Made by Joe, Last edit 2017/02/02

output: order parameters (2 textfiles)

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class OrderParameter.OrderParameter(resname, atom_A_name, atom_B_name, M_atom_A_name, M_atom_B_name, *args)

Bases: object

Class for storing&manipulating order parameter (OP) related metadata (definition, name, …) and OP trajectories and methods to evaluate OPs.

calc_OP(atoms)

calculates Order Parameter according to equation S = 1/2 * (3*cos(theta)^2 -1)

property get_avg_std_OP

Provides average and stddev of all OPs in self.traj

property get_avg_std_stem_OP

Provides average and stddev of all OPs in self.traj

property get_op_res

Provides average and stddev of all OPs in self.traj

OrderParameter.calc_angle(atoms, com)

calculates the angle between the vector and z-axis in degrees no PBC check! Calculates the center of mass of the selected atoms to invert bottom leaflet vector

OrderParameter.calc_z_dim(gro)

OrderParameter.read_trajs_calc_OPs(ordPars, top, trajs)

procedure that creates MDAnalysis Universe with top, reads in trajectories trajs and then goes through every frame and evaluates each Order Parameter “S” from the list of OPs ordPars. ordPars : list of OrderParameter class

each item in this list describes an Order parameter to be calculated in the trajectory

topstr

filename of a top file (e.g. conf.gro)

trajslist of strings

filenames of trajectories

OrderParameter.parse_op_input(fname, lipid_name)

OrderParameter.find_OP(inp_fname, top_fname, traj_fname, lipid_name)

OrderParameter.read_trj_PN_angles(molname, atoms, top_fname, traj_fname, gro_fname)

class OrderParameter.Dihedrals(resname, atom_1_name, atom_2_name, atom_3_name, atom_4_name, *args)

Bases: object

OrderParameter.parseDihedralInput(mapping_file)