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Alanine Dodecapeptide Folding

Last updated:
2024/01/01

Main topics:

1. Build an implicit-solvent model of alanine dodecapeptide with Xponge
2. Run the simulation with SPONGE 1.4
3. Visualize the results with VMD

Software Installation

See Installation on Linux and Installation on Windows.

Model Building

Open a terminal and start Python:

python

In the Python terminal, enter the following Python commands in order.

1. Import the Required Modules

import Xponge #Xponge itself
import Xponge.forcefield.amber.ff19sb  #The force field used
from Xponge.forcefield.special import gb #The implicit-solvent GB model used

2. Obtain the Xponge Molecule Instance

mol = NALA + ALA * 10 + CALA

3. Set the GB Parameters

gb.Set_GB_Radius(mol)

4. Save the Input Files

Save_PDB(mol, "ALA.pdb")
Save_SPONGE_Input(mol, "ALA")

Molecular Dynamics Simulation

In the working folder, create an mdin.txt file with your preferred text editor:

ALA12 simulation
pbc = 0
mode = NVT
dt = 2e-3
cutoff = 999
constrain_mode = SHAKE
step_limit = 5000000
thermostat = middle_langevin
default_in_file_prefix = ALA

For the meanings of these commands, see Input Commands.

Then enter the following command in the terminal:

SPONGE -mdin mdin.txt

Analysis and Discussion

Result Analysis

You can read the generated mdout.txt file to obtain the energy data. Use the following Python script to read the energy changes:

from Xponge.analysis import MdoutReader
mdout = MdoutReader("mdout.txt")
import matplotlib.pyplot as plt
plt.plot(mdout.time, mdout.potential)
plt.show()

The resulting plot is shown below:

You can also use VMD to visualize the trajectory:

vmd -sponge_mass ./ALA_mass.txt mdcrd.dat