Chapter 17: Lipid Interactions in Membranes and Monte Carlo Simulations#
Learning Objectives#
By the end of this lecture, you should be able to
Describe a coarse-grained model for lipids and its advantages in simulating lipid bilayers.
Implement a Monte Carlo simulation to study lipid interactions in a membrane.
Introduction#
Lipids are essential components of cell membranes, forming a bilayer structure that separates the cell from its environment. Understanding lipid interactions is crucial for studying membrane properties and functions. In this lecture, we will explore how to model lipid interactions using a coarse-grained approach and simulate a lipid membrane using Monte Carlo methods.
Coarse-Grained Models for Lipids#
Advantages of Coarse-Grained Models#
Coarse-grained models represent multiple atoms as a single interaction site, reducing the number of particles in the simulation. This simplification allows us to study larger systems and longer timescales than all-atom models. For lipids, coarse-grained models capture essential interactions while maintaining computational efficiency.
Tip
Coarse-grained models are also useful for studying lipid phase transitions, membrane fusion, and other membrane properties because, by capturing just the essential interactions, they allow us to efficiently and systematically test hypotheses about lipid behavior.
Cooke-WCA Model#
The Cooke-WCA Model is a coarse-grained model for lipids that captures the essential interactions between lipid head and tail groups. The model represents lipids as three particles: one head and two tails. The head-head, head-tail, and tail-tail interactions are modeled using a pair potential that includes repulsive, bond, bend, and attractive terms.
Repulsive Potential#
The repulsive potential \(V_{\mathrm{rep}}(r_{ij};b_{ij})\) prevents particles from overlapping. The potential is given by
where \(r_{ij}\) is the distance between particles \(i\) and \(j\), \(b_{ij}\) is the sum of the radii of particles \(i\) and \(j\), \(\epsilon\) is the interaction strength, and \(r_c = 2^{1/6}b_{ij}\) is the cutoff distance. The repulsive potential is zero beyond the cutoff distance, representing the hard-core diameter of the particles.
Let’s visualize the repulsive potential for different values of \(b\).
import numpy as np
import matplotlib.pyplot as plt
def repulsive_potential(r, b):
"""
Compute the repulsive potential between two particles.
Parameters
----------
r : float
Distance between particles.
b : float
Sum of the hard-core radii of the particles.
Returns
-------
potential : float
Repulsive potential between the particles.
"""
potential = np.where(
r <= 2**(1/6)*b,
4*((b/r)**12 - (b/r)**6 + 1/4),
0
)
return potential
# Define the distance range
r = np.linspace(0.5, 3, 100)
b_values = [1, 1.5, 2]
# Plot the repulsive potential for different values of b
plt.figure(figsize=(10, 6))
colors = ["C0", "C1", "C2"]
for i, b in enumerate(b_values):
plt.plot(r, repulsive_potential(r, b), label=f"b={b}", color=colors[i])
plt.axvline(2**(1/6)*b, color="k", linestyle="--")
plt.xlim(0.5, 3)
plt.ylim(-1, 5)
plt.xlabel(r"Distance ($r / \sigma$)")
plt.ylabel(r"Repulsive Potential ($V_{\mathrm{rep}} / \epsilon$)")
plt.title("Cooke-WCA Repulsive Potential")
plt.legend()
plt.show()
The plot shows that the repulsive potential increases rapidly as particles approach each other, preventing overlap due to the hard-core diameter \(b_{ij}\). The potential is zero beyond the cutoff distance, ensuring that particles do not interact beyond this range.
Note
To ensure an effective cylindrical lipid shape, we choose \(b_{\text{head,head}} = b_{\text{head,tail}} = 0.95\sigma\) and \(b_{\text{tail,tail}} = \sigma\), where \(\sigma\) is the unit of length.
Bond Potential#
The bond potential \(V_{\mathrm{bond}}(r_{ij})\) prevents particles from drifting too far apart. The potential is given by
where \(k_{\mathrm{bond}} = 30\epsilon/\sigma^2\) is the bond stiffness, \(r_{\infty} = 1.5\sigma\) is the “divergence distance,” and \(\sigma\) is the particle separation. The bond potential prevents particles from drifting too far apart. Let’s visualize the bond potential for different values of \(r_{\infty}\).
def bond_potential(r, k_bond, r_inf):
"""
Compute the bond potential between two particles.
Parameters
----------
r : float
Distance between particles.
k_bond : float
Bond stiffness.
r_inf : float
Divergence distance.
Returns
-------
potential : float
Bond potential between the particles.
"""
potential = -0.5*k_bond*r_inf**2*np.log(1 - (r/r_inf)**2)
return potential
# Define the distance range
r_min = 0.5
k_bond = 30
r_inf_values = [1, 1.25, 1.5]
# Plot the bond potential for different values of r_inf
plt.figure(figsize=(10, 6))
colors = ["C0", "C1", "C2"]
for i, r_inf in enumerate(r_inf_values):
r = np.linspace(r_min, r_inf - 0.01, 100)
plt.plot(r, bond_potential(r, k_bond, r_inf), label=f"$r_{{\\infty}}$={r_inf}", color=colors[i])
plt.axvline(r_inf, color="k", linestyle="--")
plt.xlabel(r"Distance ($r / \sigma$)")
plt.ylabel(r"Bond Potential ($V_{\mathrm{bond}} / \epsilon$)")
plt.title("FENE Bond Potential")
plt.legend()
plt.show()
The plot shows that the bond potential increases rapidly as particles drift apart, preventing them from moving beyond the divergence distance \(r_{\infty}\). The potential is infinite at \(r_{\infty}\), ensuring that particles remain within a certain range.
FENE Potential
The bond potential is based on the FENE (Finite Extensible Nonlinear Elastic) model, which is commonly used to model bond stretching in polymer chains. The FENE potential prevents bond lengths from exceeding a critical value, ensuring the stability of the polymer chain. For more details, see:
Kremer, K.; Grest, G. S. Dynamics of Entangled Linear Polymer Melts: A Molecular-Dynamics Simulation. The Journal of Chemical Physics 1990, 92 (8), 5057–5086. https://doi.org/10.1063/1.458541.
Bend Potential#
The bend potential \(V_{\mathrm{bend}}(r_{ij})\) promotes a preferred angle between particles. The potential is given by
where \(k_{\mathrm{bend}} = 10\epsilon/\sigma^2\) is the bending stiffness. The bend potential favors a preferred angle between particles, promoting a straight configuration. Let’s calculate the bend potential for different angles.
def bend_potential(r, sigma, k_bend):
"""
Compute the bend potential between two particles.
Parameters
----------
r : float
Distance between particles.
sigma : float
Unit of length.
k_bend : float
Bending stiffness.
Returns
-------
potential : float
Bend potential between the particles.
"""
potential = 0.5*k_bend*(r - 4*sigma)**2
return potential
# Define the distance range
r = np.linspace(3, 5, 100)
sigma = 1
k_bend = 10
# Plot the bend potential
plt.figure(figsize=(10, 6))
plt.plot(r, bend_potential(r, sigma, k_bend), color="C0")
plt.axvline(4*sigma, color="k", linestyle="--")
plt.xlabel("Distance ($r$)")
plt.ylabel(r"Bend Potential ($V_{\mathrm{bend}} / \epsilon$)")
plt.title("Bend Potential")
plt.show()
The plot shows that the bend potential increases as the angle deviates from the preferred value, favoring a straight configuration. The potential is zero at the preferred angle, ensuring that particles maintain the desired orientation.
Attractive Potential#
The attractive potential \(V_{\mathrm{attr}}(r_{ij})\) promotes interactions between lipid tails, leading to lipid aggregation. The attractive potential is given by
where \(w_c\) is the attractive range. The attractive potential favors interactions within a specific distance range, promoting lipid aggregation. Let’s visualize the attractive potential for different values of \(w_c\).
def attractive_potential(r, r_c, w_c):
"""
Compute the attractive potential between two particles.
Parameters
----------
r : float
Distance between particles.
r_c : float
Cutoff distance.
w_c : float
Attractive range.
Returns
-------
potential : float
Attractive potential between the particles.
"""
potential = np.where(
r < r_c,
-1,
np.where(
r <= r_c + w_c,
-1*np.cos(np.pi*(r - r_c)/(2*w_c))**2,
0
)
)
return potential
# Define the distance range
r = np.linspace(0.5, 3, 100)
r_c = 1
w_c_values = [0.5, 1, 1.5, 2]
# Plot the attractive potential for different values of w_c
plt.figure(figsize=(10, 6))
colors = ["C0", "C1", "C2", "C3"]
for i, w_c in enumerate(w_c_values):
plt.plot(r, attractive_potential(r, r_c, w_c), label=f"$w_c$={w_c}", color=colors[i])
plt.axvline(r_c, color="k", linestyle="--")
plt.axvline(r_c + w_c, color="k", linestyle="--")
plt.xlim(0.5, 3)
plt.ylim(-1, 0)
plt.xlabel(r"Distance ($r / \sigma$)")
plt.ylabel(r"Attractive Potential ($V_{\mathrm{attr}} / \epsilon$)")
plt.title("Attractive Potential")
plt.legend()
plt.show()
The plot shows that the attractive potential promotes interactions within a specific distance range, favoring lipid aggregation. The potential is zero beyond the attractive range, ensuring that interactions do not occur beyond this distance.
Total Potential#
The total potential \(V_{\mathrm{total}}(r_{ij})\) is the sum of the repulsive, bond, bend, and attractive potentials for all particle pairs.
where \(\mathbf{r}\) is the configuration of all particles, \(r_{\mathrm{lipid,bond}}\) is the distance between a particle and its bonded particle in the same lipid, and \(r_{\mathrm{lipid,bend}}\) is the distance between a head particle and the second tail particle in the same lipid.
Testing the Total Potential#
Let’s test the total potential for a simple configuration of two tail particles with a separations of \(\sigma\).
# Calculate the repulsive potential
r = 1 # Separation between particles in sigma
b = 1 # Sum of the hard-core radii of the particles in sigma
print(f"Repulsive Potential: {repulsive_potential(1, 1):.2f} (expected: 1.00)")
# Calculate the bond potential
k_bond = 30 # Bond stiffness in epsilon/sigma^2
r_inf = 1.5 # Divergence distance in sigma
print(f"Bond Potential: {bond_potential(r, k_bond, r_inf):.2f} (expected: 19.84)")
# Calculate the attractive potential
r_c = 2**(1/6) # Cutoff distance in sigma
w_c = 1 # Attractive range in sigma
print(f"Attractive Potential: {attractive_potential(r, r_c, w_c):.2f} (expected: -1.00)")
Repulsive Potential: 1.00 (expected: 1.00)
Bond Potential: 19.84 (expected: 19.84)
Attractive Potential: -1.00 (expected: -1.00)
Building a Lipid Bilayer#
To build a lipid bilayer, we need to create a system of lipids with head and tail particles. We will use the Cooke-WCA model to represent the interactions between lipids. Let’s define the parameters for the Cooke-WCA model.
# Define the Cooke-WCA parameters
b_head_head = 0.95 # Sum of the hard-core radii for head-head interactions
b_head_tail = 0.95 # Sum of the hard-core radii for head-tail interactions
b_tail_tail = 1.0 # Sum of the hard-core radii for tail-tail interactions
k_bond = 30.0 # Bond stiffness
r_inf = 1.5 # Divergence distance
k_bend = 10.0 # Bending stiffness
r_c = 2**(1/6) # Cutoff distance for attractive potential
w_c = 1.0 # Attractive range
Building One Lipid#
Let’s build a single lipid with one head and two tail particles. We will define the particle positions and visualize the lipid configuration.
import matplotlib.patches as patches
# Define the particle positions for one lipid
head = np.array([0, 0])
tail1 = head + np.array([b_head_tail, 0])
tail2 = tail1 + np.array([b_tail_tail * np.cos(np.pi/3), b_tail_tail * np.sin(np.pi/3)])
# Plot the lipid configuration
plt.figure(figsize=(6, 3))
plt.plot(*head, "o", color="C0", label="Head")
plt.plot(*tail1, "o", color="C1", label="Tail 1")
plt.plot(*tail2, "o", color="C2", label="Tail 2")
plt.plot([head[0], tail1[0]], [head[1], tail1[1]], "k-")
plt.plot([tail1[0], tail2[0]], [tail1[1], tail2[1]], "k-")
plt.gca().add_patch(patches.Circle(head, 19 / 40, edgecolor="k", facecolor="none"))
plt.gca().add_patch(patches.Circle(tail1, 19 / 40, edgecolor="k", facecolor="none"))
plt.gca().add_patch(patches.Circle(tail2, 21 / 40, edgecolor="k", facecolor="none"))
plt.xlim(-5, 5)
plt.ylim(-5, 5)
plt.gca().set_aspect("equal", adjustable="box")
plt.xlabel("$x$")
plt.ylabel("$y$")
plt.title("Lipid Configuration")
plt.legend()
plt.show()
Optimizing the Lipid’s Geometry#
To optimize the lipid’s geometry, we need to minimize the total potential \(V_{\mathrm{total}}(r_{ij})\) by adjusting the particle positions. We will use the L-BFGS-B algorithm to minimize the potential and visualize the optimized lipid configuration.
from scipy.optimize import minimize
def one_lipid_potential(positions, b_head_head, b_head_tail, b_tail_tail, k_bond, r_inf, k_bend, r_c, w_c):
"""
Compute the total potential for one lipid.
Parameters
----------
positions : array_like
Particle positions for one lipid.
b_head_head : float
Sum of the hard-core radii for head-head interactions.
b_head_tail : float
Sum of the hard-core radii for head-tail interactions.
b_tail_tail : float
Sum of the hard-core radii for tail-tail interactions.
k_bond : float
Bond stiffness.
r_inf : float
Divergence distance.
k_bend : float
Bending stiffness.
r_c : float
Cutoff distance for attractive potential.
w_c : float
Attractive range.
Returns
-------
potential : float
Total potential for one lipid.
"""
head, tail1, tail2 = positions.reshape((3, 2))
r_head_tail1 = np.linalg.norm(head - tail1)
r_head_tail2 = np.linalg.norm(head - tail2)
r_tail1_tail2 = np.linalg.norm(tail1 - tail2)
potential = (
repulsive_potential(r_head_tail1, b_head_tail) +
repulsive_potential(r_head_tail2, b_head_tail) +
repulsive_potential(r_tail1_tail2, b_tail_tail) +
bond_potential(r_head_tail1, k_bond, r_inf) +
bond_potential(r_tail1_tail2, k_bond, r_inf) +
bend_potential(r_head_tail2, 1, k_bend) +
attractive_potential(r_tail1_tail2, r_c, w_c)
)
return potential
# Define the initial particle positions for one lipid
initial_positions = np.array([head, tail1, tail2]).flatten()
# Minimize the total potential for one lipid
result = minimize(one_lipid_potential, initial_positions, args=(b_head_head, b_head_tail, b_tail_tail, k_bond, r_inf, k_bend, r_c, w_c), method="L-BFGS-B")
optimized_positions = result.x.reshape((3, 2))
# Plot the optimized lipid configuration
plt.figure(figsize=(6, 3))
plt.plot(*optimized_positions[0], "o", color="C0", label="Head")
plt.plot(*optimized_positions[1], "o", color="C1", label="Tail 1")
plt.plot(*optimized_positions[2], "o", color="C2", label="Tail 2")
plt.plot([optimized_positions[0][0], optimized_positions[1][0]], [optimized_positions[0][1], optimized_positions[1][1]], "k-")
plt.plot([optimized_positions[1][0], optimized_positions[2][0]], [optimized_positions[1][1], optimized_positions[2][1]], "k-")
plt.gca().add_patch(patches.Circle(optimized_positions[0], 19 / 40, edgecolor="k", facecolor="none"))
plt.gca().add_patch(patches.Circle(optimized_positions[1], 19 / 40, edgecolor="k", facecolor="none"))
plt.gca().add_patch(patches.Circle(optimized_positions[2], 21 / 40, edgecolor="k", facecolor="none"))
plt.xlim(-5, 5)
plt.ylim(-5, 5)
plt.gca().set_aspect("equal", adjustable="box")
plt.xlabel("$x$")
plt.ylabel("$y$")
plt.title("Optimized Lipid Configuration")
plt.legend()
plt.show()
Building a Lipid Monolayer#
To build a lipid monolayer, we need to create a system of lipids with head and tail particles. We will optimize the lipid geometry and visualize the monolayer configuration.
def build_lipid_monolayer(n_lipids, b_head_head, b_head_tail, b_tail_tail, k_bond, r_inf, k_bend, r_c, w_c):
"""
Build a lipid monolayer with the specified number of lipids.
Parameters
----------
n_lipids : int
Number of lipids in the monolayer.
b_head_head : float
Sum of the hard-core radii for head-head interactions.
b_head_tail : float
Sum of the hard-core radii for head-tail interactions.
b_tail_tail : float
Sum of the hard-core radii for tail-tail interactions.
k_bond : float
Bond stiffness.
r_inf : float
Divergence distance.
k_bend : float
Bending stiffness.
r_c : float
Cutoff distance for attractive potential.
w_c : float
Attractive range.
Returns
-------
lipid_positions : array_like
Particle positions for the lipid monolayer.
"""
np.random.seed(42)
lipid_positions = []
for i in range(n_lipids):
head = np.array([i * b_head_tail, 0]) + np.random.uniform(-0.05, 0.05, 2)
tail1 = head - np.array([0, b_head_tail]) + np.random.uniform(-0.05, 0.05, 2)
theta = np.random.uniform(7*np.pi/16, 9*np.pi/16)
tail2 = tail1 - np.array([b_tail_tail * np.cos(theta), b_tail_tail * np.sin(theta)]) + np.random.uniform(-0.05, 0.05, 2)
lipid_positions.extend([head, tail1, tail2])
return np.array(lipid_positions)
# Build a lipid monolayer with 10 lipids
n_lipids = 10
lipid_positions = build_lipid_monolayer(n_lipids, b_head_head, b_head_tail, b_tail_tail, k_bond, r_inf, k_bend, r_c, w_c)
# Plot the lipid monolayer configuration
plt.figure(figsize=(6, 3))
for i in range(n_lipids):
head, tail1, tail2 = lipid_positions[i*3:(i+1)*3]
plt.plot(*head, "o", color="C0")
plt.plot(*tail1, "o", color="C1")
plt.plot(*tail2, "o", color="C2")
plt.plot([head[0], tail1[0]], [head[1], tail1[1]], "k-")
plt.plot([tail1[0], tail2[0]], [tail1[1], tail2[1]], "k-")
plt.gca().add_patch(patches.Circle(head, 19 / 40, edgecolor="k", facecolor="none"))
plt.gca().add_patch(patches.Circle(tail1, 19 / 40, edgecolor="k", facecolor="none"))
plt.gca().add_patch(patches.Circle(tail2, 21 / 40, edgecolor="k", facecolor="none"))
plt.gca().set_aspect("equal", adjustable="box")
plt.xlabel("$x$")
plt.ylabel("$y$")
plt.title("Lipid Monolayer Configuration")
plt.show()
Equilibrating the Lipid Monolayer#
To equilibrate the lipid monolayer, we will perform a Metropolis Monte Carlo simulation to sample lipid configurations. We will implement the Metropolis algorithm to accept or reject moves based on the total potential \(V_{\mathrm{total}}(r_{ij})\).
def lipid_monolayer_potential(positions, n_lipids, b_head_head, b_head_tail, b_tail_tail, k_bond, r_inf, k_bend, r_c, w_c):
"""
Compute the total potential for a lipid monolayer.
Parameters
----------
positions : array_like
Particle positions for the lipid monolayer.
n_lipids : int
Number of lipids in the monolayer.
b_head_head : float
Sum of the hard-core radii for head-head interactions.
b_head_tail : float
Sum of the hard-core radii for head-tail interactions.
b_tail_tail : float
Sum of the hard-core radii for tail-tail interactions.
k_bond : float
Bond stiffness.
r_inf : float
Divergence distance.
k_bend : float
Bending stiffness.
r_c : float
Cutoff distance for attractive potential.
w_c : float
Attractive range.
Returns
-------
potential : float
Total potential for the lipid monolayer.
"""
n_particles = n_lipids * 3
# Compute V_rep for all particle pairs
V_rep = 0
for i in range(n_particles):
for j in range(i + 1, n_particles):
r = np.linalg.norm(positions[i] - positions[j])
# Determine the particle types
if i % 3 == 0 and j % 3 == 0:
b = b_head_head
elif i % 3 == 0 or j % 3 == 0:
b = b_head_tail
else:
b = b_tail_tail
V_rep += repulsive_potential(r, b)
# Compute V_bond for bonded particles
V_bond = 0
for i in range(0, n_particles, 3):
r_head_tail1 = np.linalg.norm(positions[i] - positions[i + 1])
r_tail1_tail2 = np.linalg.norm(positions[i + 1] - positions[i + 2])
V_bond += bond_potential(r_head_tail1, k_bond, r_inf)
V_bond += bond_potential(r_tail1_tail2, k_bond, r_inf)
# Compute V_bend for head-tail-tail angles
V_bend = 0
for i in range(0, n_particles, 3):
r_head_tail2 = np.linalg.norm(positions[i] - positions[i + 2])
V_bend += bend_potential(r_head_tail2, 1, k_bend)
# Compute V_attr for tail-tail interactions
V_attr = 0
for i in range(2, n_particles, 3):
for j in range(i + 3, n_particles, 3):
r = np.linalg.norm(positions[i] - positions[j])
V_attr += attractive_potential(r, r_c, w_c)
potential = V_rep + V_bond + V_bend + V_attr
return potential
def metropolis_mc(positions, n_lipids, b_head_head, b_head_tail, b_tail_tail, k_bond, r_inf, k_bend, r_c, w_c, n_steps, temperature):
"""
Perform a Metropolis Monte Carlo simulation for a lipid monolayer.
Parameters
----------
positions : array_like
Initial particle positions for the lipid monolayer.
n_lipids : int
Number of lipids in the monolayer.
b_head_head : float
Sum of the hard-core radii for head-head interactions.
b_head_tail : float
Sum of the hard-core radii for head-tail interactions.
b_tail_tail : float
Sum of the hard-core radii for tail-tail interactions.
k_bond : float
Bond stiffness.
r_inf : float
Divergence distance.
k_bend : float
Bending stiffness.
r_c : float
Cutoff distance for attractive potential.
w_c : float
Attractive range.
n_steps : int
Number of Monte Carlo steps.
temperature : float
Temperature of the system.
Returns
-------
positions : array_like
Final particle positions for the lipid monolayer.
"""
beta = 1 / temperature
n_particles = n_lipids * 3
trajectory = np.zeros((n_steps, n_particles, 2))
energies = np.zeros(n_steps)
for step in range(n_steps):
# Randomly select a particle to move
i = np.random.randint(n_particles)
move = np.random.uniform(-0.1, 0.1, 2)
new_positions = positions.copy()
new_positions[i] += move
# Compute the change in potential
delta_potential = lipid_monolayer_potential(new_positions, n_lipids, b_head_head, b_head_tail, b_tail_tail, k_bond, r_inf, k_bend, r_c, w_c) - lipid_monolayer_potential(positions, n_lipids, b_head_head, b_head_tail, b_tail_tail, k_bond, r_inf, k_bend, r_c, w_c)
# Accept or reject the move
if delta_potential < 0 or np.random.rand() < np.exp(-beta * delta_potential):
positions = new_positions
# Store the particle positions
trajectory[step] = positions
# Compute the total energy
energies[step] = lipid_monolayer_potential(positions, n_lipids, b_head_head, b_head_tail, b_tail_tail, k_bond, r_inf, k_bend, r_c, w_c)
return positions, trajectory, energies
# Equilibrate the lipid monolayer
n_steps = 1000
temperature = 1.0
equilibrated_positions, trajectory, energies = metropolis_mc(lipid_positions, n_lipids, b_head_head, b_head_tail, b_tail_tail, k_bond, r_inf, k_bend, r_c, w_c, n_steps, temperature)
# Plot the equilibrated lipid monolayer configuration and energy
fig, axs = plt.subplots(1, 2, figsize=(12, 6))
for i in range(n_lipids):
head, tail1, tail2 = equilibrated_positions[i*3:(i+1)*3]
axs[0].plot(*head, "o", color="C0")
axs[0].plot(*tail1, "o", color="C1")
axs[0].plot(*tail2, "o", color="C2")
axs[0].plot([head[0], tail1[0]], [head[1], tail1[1]], "k-")
axs[0].plot([tail1[0], tail2[0]], [tail1[1], tail2[1]], "k-")
axs[0].add_patch(patches.Circle(head, 19 / 40, edgecolor="k", facecolor="none"))
axs[0].add_patch(patches.Circle(tail1, 19 / 40, edgecolor="k", facecolor="none"))
axs[0].add_patch(patches.Circle(tail2, 21 / 40, edgecolor="k", facecolor="none"))
axs[0].set_aspect("equal", adjustable="box")
axs[0].set_xlabel("$x$")
axs[0].set_ylabel("$y$")
axs[0].set_title("Equilibrated Lipid Monolayer Configuration")
axs[1].plot(energies, color="C0")
axs[1].set_xlabel("Step")
axs[1].set_ylabel("Energy")
axs[1].set_title("Energy vs. Step")
plt.tight_layout()
plt.show()
