MD Simulation

The most important goal of MD simulation is to capture realistic movements of protein that we would observe in the human body (which is critical, for example, for calculation of a drug binding affinity). In the pursuit of this goal, we start with a realistic MD simulation system (with water molecules, lipid molecules for the bilayer, and ions) and run a 1-100 ns simulation. We call this a "production run". In our lab, CHARMM-GUI and Desmond are used to prepare MD simulation systems together with experimental strucutres of protein or molecular models built by us. In either case, the initial MD system is not realistic enough for a production run and must go through equilibration.

You can run MD simulations on the local computers in Rm 512 of Timken-Burnett Research Building, KCOM, ATSU or on Bridges at the Pittsburgh Supercomputing Center using Gromacs. In order to access Bridges, first you must create an account at Xsede. Before you run your simulations, you should benchmark your system first.

The data for simulated annealing are found on the Google Drive (Norimatsu Lab > CFTR Projects > MD Simulations > Simulated Annealing). The folder called "Data-Open" is for an open homology model of CFTR. There are SA runs for 150 mM and 1M KCl. Two temperatures (400 and 500K) were used for each concentration. The folder called "Data-6MSM" is for SA runs with the cryo-EM structure 6MSM.