A Variety of Initial Velocities in Restarting Molecular Dynamics Simulations Promotes Protein Transitions

The key to efficiently promoting protein transitions in conformational sampling is to regenerate the initial velocities reasonably. The present study assessed how the conformational resampling promotes protein transitions depending on four initial velocity regeneration protocols: regeneration based on the Maxwell -Boltzmann distribution, orthogonalized regeneration, regeneration at a high temperature, and their mixture. In con-clusion, protein transitions can be efficiently promoted using orthogonalized velocities after their regeneration at a high temperature.