The intermediate fold state for Chicken Villin HP-36 obtained from molecular dynamics simulation (Duan and Kollman 1998).

With ajith gunaratne, Junkoo Park

The molecular dynamics simulation method can be used to study various dynamic properties of proteins, but a long sequence of iterations has to be carried out even for small protein motions due to the small time step (1e-15sec) required. The bonding forces are among those causing the fast protein vibrations that require small time steps to integrate, and they may be replaced by a set of bond length constraints, to increase the step size and hence the simulation speed. Lagrange multiplier methods have been developed for constrained dynamics simulation. In these methods, the multipliers are determined in every step to satisfy the constraints via the solution of a nonlinear system of equations.  

 

Constrained molecular dynamics