Second program for a class in molecular modelling (done in june 2016). It carries out a Monte Carlo simulation with simulated annealing for HP protein model.
HP model simplifies protein sequence to only P and H letters that mean "Polar" and "Hydrophobic".
You can manually input your simplified peptide model (HP model) in main.py script and then run python main.py. It will carry out a Monte Carlo simulation with simulated annealing where starting temperature is T=1 and finishing one is 0.15, with change in every cycle by -0.05. For every temperature there are carried out K=10000 steps (accepting or not the allowed conformation). Simulation starts from a line conformation of peptide.
You can change the input parameters in the simulation.py file.
After the simulation there will be a lot of files generated which are:
- graph representing specific heat per temperature
- graph with mean moment of intertia (gyration radius) per temperature
- histograms of number of contacts for each temperature
- text files with statistics
- best.pdb file with a model for a start conformation and one of conformations with best number of contacs for each temperature
(example in ./1)