Distance Between Pores

Calculate the pore-to-pore distance from an MD trajectory of an HII LLC membrane

usage: p2p.py [-h] [-t TRAJ] [-g GRO] [-begin BEGIN] [-end END] [-skip SKIP]
              [-p PORES] [-c COMPONENT [COMPONENT ...]] [-E EQUIL]
              [-x EXCLUDE [EXCLUDE ...]] [--auto_exclude] [-b NBOOT]
              [--plot_every PLOT_EVERY] [--noshow] [--save] [--plot_avg]
              [--plot_std] [-T T] [--buffer BUFFER]

Named Arguments

-t, --traj

Path to input file

Default: “PR.trr”

-g, --gro

Coordinate configuration file (.gro, .pdb)

Default: “berendsen.gro”

-begin, --begin
 

Frame to begin calculations

Default: 0

-end, --end

Frame to stop calculations

Default: -1

-skip, --skip

Sample every nth frame

Default: 1

-p, --pores

Number of pores in unit cell

Default: 4

-c, --component
 

Name of monomer component used to track pore positions. This script will calculate the average coordinate of each in each pore. Special predefined cases include: “tails”, “Tails”, “benzene”, “Benzene”, “Head Groups, “tail_ends”, “tail_fronts”, “Sodium”. These are specific to Na-GA3C11

Default: “NA”

-E, --equil

Frame number where system is equilibrated. “auto” will use pymbar.timeseries.DetectEquilibration to determine which frame to start at. It is often worth double checking its choice manually

Default: “auto”

-x, --exclude

Index of p2p distance to exclude as written inthe list: [“1-2”, “1-3”, “1-4”, “2-3”, “2-4”, “3-4”]

Default: [4]

--auto_exclude

Specifying this will override args.exclude and decide which pore-to-pore distance to exclude automatically by dropping the highest value

Default: False

-b, --nboot

Number of bootstrap trials for generating statistics

Default: 2000

--plot_every

Plot every n frames

Default: 1

--noshow

Specify this flag to prevent the plot from showing

Default: False

--save

Save the output plot

Default: False

--plot_avg

Plot average p2p distance at each frame

Default: False

--plot_std

Plot average p2p distance at each frame

Default: False

-T Use for concatenated trajectories of simulations run at multiple temperatures. Supply the name of index file (ascii format) with temperatures and times where the switch occurs. On each line supply the info with the format temp:time
--buffer

Fraction (of membrane thickness) of top and bottom ofmembrane to exclude from p2p calculations. Useful if you solvate both sides with water andions float into solution.

Default: 0

Functions

p2p.restrict_atoms(t, component)

Restrict trajectory of coordinates to selected atoms

Parameters:
  • t (mdtraj.core.trajectory.Trajectory) – mdtraj trajectory object
  • component (str or list) – names of components to be used for tracking pore centers.
Returns:
p2p.avg_pore_loc(npores, pos, buffer=0)

Calculate average pore location for each pore at each frame

Parameters:
  • no_pores (int) – the number of pores in the unit cell
  • pos (numpy.ndarray, shape(ncomponents, 3) or numpy.ndarray, shape(nframes, ncomponents, 3)) – the coordinates of the component(s) which you are using to locate the pore centers
  • buffer (float) – fraction (of membrane thickness) of top and bottom of membrane to exclude from p2p calculations
Returns:

numpy array containing the x, y coordinates of the center of each pore at each frame
p2p.p2p(p_centers, distances)

Calculate all pairwise pore-to-pore distances (4 pores is the only number of pores implemented currently)

Parameters:
  • p_centers (numpy.ndarray, shape(p_centers.shape[0], p_centers.shape[1], 2)) – the x, y locations of the pore centers
  • distances (int) – the number of distinct distances between pores
Returns:

(np.ndarray, shape(p_centers.shape[0], distances, 2) All frame-by-frame pore-to-pore distances
p2p.p2p_stats(p2ps, exclude, nboot, equil)

Calculate the average and spread of pore-to-pore distances

Parameters:
  • p2ps (numpy.ndarray, shape(nframes, np2p_distances)) – all of the pore-to-pore distances
  • exclude (int or str) – exclude a certain pore-to-pore interaction (such as the distance from pores on opposite sides of a parallelogram as is the case in a hexagonal system). If ‘auto’, then exclude will be automatically selected
  • nboot (int) – number of bootstrap trials to use when generating statistics
  • equil (int or str) – the trajectory frame at which to start generating statistics. Care about this parameter if you choose to detect equilibration manually. Otherwise ‘auto’ will use pymbar to find it for you
Returns:

the average and standard deviation of pore to pore distances