Simulation of protein molecular dynamics

Availability of supercomputers and development of elegant molecular methods of dynamics simulation have been made a basis for the employment of explosive methods and a wide range of successful applications (Karplus and Petsko, 1990). The computer simulation produces individual particle motions as a function of time followed by the examination of specific contributions to the process. 

Dynamic simulation for a protein includes the following steps  

2) A set of atomic coordinates is obtained from X-ray crystallographic or NMR structure data, or by model building. The structure is first refined to relieve local stresses due to overlaps ofnon-bonded atoms, bond-length and angles distortions, etc. 

3) Using the classic Newton s law Fj = nijxaj (F , mj and a are the force on the atom, its mass, and its acceleration, respectively) and taking into consideration a Maxwellian distribution for a given temperature, a simulation of the atoms velocities is performed for a few picoseconds. 

4) For relatively small proteins, like myoglobin, about 1,000 water molecules can be included in the calculation. For large proteins, simplified treatments are used. A set of 

---

Conformational Dynamics Simulations of Proteins molecular dynamics conformational flooding... 

---