Tutorial #4: Residence Time Calculations

In this tutorial, we will explore how to compute residence times for specific interactions. Residence time calculations are crucial for understanding the stability of molecular interactions in your simulations.

Prerequisites

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

Understanding Residence Time Calculations

Residence time calculations involve determining how long a specific molecular interaction persists in your simulation. In this tutorial, we will calculate the residence time for residue 401 in contact with cholesterol (CHOL).

Setting Up Parameters

To compute residence time, we need to define some parameters related to the simulation data. These parameters include the total simulation time and the time step.

# Calculate total simulation time and time step
totaltime = u.trajectory.totaltime * u.params['unit_conversion_factor']
timestep = round(u.trajectory.dt * u.params['unit_conversion_factor'], 4)

print("Total Simulation Time: {} units".format(totaltime))
print("Time Step: {} units".format(timestep))

These parameters are essential for the residence time calculation.

Computing Residence Time

Now, let’s compute the residence time for residue 401 in contact with cholesterol (CHOL). We will use the KoffCalculator class from the prolint2.metrics.restime module.

# Get the data for residue 401 with CHOL
data = c.contacts[401]['CHOL']

# Compute residence time using KoffCalculator
r401_chol = KoffCalculator(data, totaltime, timestep, fitting_func_name='bi_expo')

print("Residence Time (koff): {} units".format(r401_chol.koff))
print("Residence Time (tau): {} units".format(r401_chol.res_time))

In this example, we use the bi_expo fitting function to calculate residence time. The KoffCalculator class takes the contact data, total simulation time, time step, and fitting function as inputs to compute the residence time.