The application of long time molecular dynamics for enhanced conformational sampling in biomolecular system was investigated. The technique was applicable to provide insufficient sampling to impact studies of the 200-300 residue proteins. It was observed that the integrators are restricted by resonance phenomena to small times steps much slower than the time scales of important structural and solvent rearrangments. In this technique, a novel set of equations of motion and a reversible, resonance free integrator were designed which permit step size on the order of 100 fs to be used.
ASJC Scopus subject areas
- Physics and Astronomy(all)