Tutorial on the usage of ecc_micelle

This tutorial shows how to use the ecc_micelle class to compute the eccentricity of a micelle that is broken across the periodic boundary conditions (PBC) at some time steps. Please note that this class can be used in the same way for aggregates that are not broken across the PBC.

Before starting any analysis, load the neccesary modules for this class.

from  utils_mda import MDA_input
#from pysoftk.pol_analysis.tools.utils_mda import MDA_input
from utils_tools import *
#from pysoftk.pol_analysis.tools.utils_tools import *
from clustering import SCP
#from pysoftk.pol_analysis.clustering import SCP
from make_micelle_whole import micelle_whole
#from pysoftk.pol_analysis.make_micelle_whole import micelle_whole
from ecc_micelle import ecc
#from pysoftk.pol_analysis.ecc_micelle import ecc

import numpy as np
import pandas as pd

  1. First load the trajectory, we are going to use the cyclic topology used in previous tutorials.

topology='data/short_movie_cyclic.tpr'
trajectory='data/short_movie_cyclic.xtc'

  1. Import the clustering data from SCP function

resids_total='data/pictures_tutorial/cyclic_scp_result.parquet'

  1. Obtain the largest micelle from the clustering pandas dataframe

largest_micelle_resids = micelle_whole(topology, trajectory).obtain_largest_micelle_resids(resids_total)

  1. Now, obtain the positions of the whole micelle

#select the resname of the polymers
resname=['LIG']

#run to obtain the whole positions
start=0
stop=10001
step=1

#run micelle_whole
atom_pos = micelle_whole(topology, trajectory).running_make_cluster_whole(resname, largest_micelle_resids, start, stop, step)

  0%|                                                                                                                                                    | 0/3 [00:00<?, ?it/s]/home/raquellrdc/Desktop/PhD/pysoftk/alejandro_newest_releast_check/pysoftk_analysis_code/test_final/make_micelle_whole.py:347: FutureWarning: arrays to stack must be passed as a "sequence" type such as list or tuple. Support for non-sequence iterables such as generators is deprecated as of NumPy 1.16 and will raise an error in the future.
  atom_positions_over_trajectory = list(tqdm(map(self.make_cluster_whole, frames, resname, cluster_resids_f[0],
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Elapsed time for matrix calculation: 0.5386 seconds

  1. We have all the neccesary inputs to run the eccentricity calculation

ecc_micelle_whole = ecc(topology, trajectory).running_ecc(largest_micelle_resids, atom_pos, start, stop, step)
ecc_micelle_whole

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[0.31216114645263193, 0.09429518042597795, 0.0661655070142777]

That is it! ecc_micelle_whole contains the eccentricity of the micelle for the selected timesteps