Tutorial #2: prolint2 Universe Properties#

In this tutorial, we will explore how to access and modify the properties of the Universe object to customize your analysis of lipid-protein interactions. You will learn how to adjust parameters such as units, normalization methods, and more to gain a deeper understanding of your molecular dynamics simulations.

Prerequisites#

Before we begin, make sure you have prolint2 installed in your Python environment.

from prolint2 import Universe
from prolint2.sampledata import GIRKDataSample
GIRK = GIRKDataSample()
u = Universe(GIRK.coordinates, GIRK.trajectory)

Displaying Current Universe Properties#

Let’s start by displaying the current properties of the Universe object using the params attribute. These properties include units, normalization methods, conversion factors, and more.

# Display the current properties of the Universe object
u.params

Here’s a breakdown of the parameters and their meanings:

  • units: This parameter determines the unit in which the results will be displayed.

  • normalizer: It defines how the results are normalized, with options for ‘counts’ (raw frame counts), ‘actual_time’ (normalized by the true simulation time), and ‘time_fraction’ (normalized by fractions of time spent in contact).

  • unit_conversion_factor: This factor converts raw counts to the desired unit.

  • norm_factor: This factor is updated based on the chosen normalization type.

Computing Contacts with Default Parameters#

Before modifying the parameters, let’s compute contacts with the default settings. Contacts are measured as contact durations relative to the total simulation time and expressed in microseconds (us).

# Compute contacts with default parameters
default = u.compute_contacts(cutoff=7)

# Access contacts for a specific residue (e.g., residue 17 from 'POPE')
residue17_default_contacts = default.contacts.get(17).get('POPE')

# Display the first 5 contact durations
residue17_default_contacts[:5]

Changing Universe Parameters and Re-computing Contacts#

Now, let’s modify the Universe parameters to suit your analysis needs.

  1. Change the Normalization Method

We will switch from ‘time_fraction’ to ‘actual_time’ for normalization. This will represent contact durations in relation to the actual time of the trajectory.

# Change the normalization method to 'actual_time'
u.normalize_by = 'actual_time'

# Display the updated parameters
u.params

Notice how the norm_factor is updated based on the chosen normalization type.

  1. Change the Units

Let’s change the units from microseconds (us) to nanoseconds (ns) to measure contact durations in their true simulation time.

# Change the units to nanoseconds
u.units = 'ns'

# Display the updated parameters
u.params

Notice how both the unit_conversion_factor and norm_factor are adjusted based on the chosen units.

Re-compute Contacts with Modified Parameters#

Now, let’s re-compute the contacts with the adjusted parameters.

# Re-compute contacts with the modified parameters
updated = u.compute_contacts(cutoff=7)

# Access contacts for the same residue (e.g., residue 17 from 'POPE')
residue17_modified_contacts = updated.contacts.get(17).get('POPE')

# Display the first 5 contact durations
residue17_modified_contacts[:5]

Congratulations! You’ve successfully modified Universe properties to customize the analysis of lipid-protein interactions in prolint2. This flexibility allows you to adapt your analysis to different conditions and represent your results in the most informative way for your research or simulation requirements.