People who know vmd and namd programs and have it installed on their computer can solve it.

1) One of the protein structures determined from the Protein Data Bank (PDB, https://www.rcsb.org/) is selected and downloaded. The PDB numbers of the proteins that can be selected are as follows: 2QHO, 6NXL, 3PSM, 2UWR, 6UMV, 2FRG, 5DZO, 5TNW, 1OOH, 2A8F 2) The general properties of the downloaded protein and what it is used for at the molecular level (what its function is) are determined. The relevant literature is reviewed and included in the project report. 3) Preparation of protein structure for s imulation using VMD program: a) Hydrogen atoms not found in crystal structures are added to the protein structure and PSF (Protein structure file) and PDB (Protein coordinate file) files are created. b) It is placed in a water box large enough to contain the created system. c) The system is neutralized and ions are added to provide physiological conditions (150 mM NaCl) 4) The simulation of the system prepared using the NAMD program is performed at 300K and 400K temperatures. Each simulation length should be at least 5 ns. Before the simulations, the minimization and equilibration phases must be performed. 5) Obtained simulation results are analyzed. In these analyzes, the kinetic energy, pressure, volume and temperature changes of the system are plotted ov er time. In addition, their distributions are compared for the 300K and 400K temperature values at which the simulation is performed. The differences observed are evaluated in terms of thermodynamics. 6) Root mean square deviation (RMSD) values of the systems are calculated and compared. Then, by calculating the RMSD value for each amino acid, the mobile regions of the protein are determined and displayed visually. 7) Transactions are prepared in report format within the framework of the headings of “Ab stract, Introduction, Method/Methodology, Conclusion and Discussion, References”.