Conformational flooding

Grubmiiller, 1995] Grubmiiller, H. Predicting slow structural transitions in macromolecular systems Conformational Flooding. Phys. Rev. E. 52 (1995) 2893-2906... 

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

Fig. 10. Conformational flooding accelerates conformational transitions and makes them accessible for MD simulations. Top left snapshots of the protein backbone of BPTI during a 500 ps-MD simulation. Bottom left a projection of the conformational coordinates contributing most to the atomic motions shows that, on that MD time scale, the system remains in its initial configuration (CS 1). Top right Conformational flooding forces the system into new conformations after crossing high energy barriers (CS 2, CS 3,. . . ). Bottom right The projection visualizes the new conformations they remain stable, even when the applied flooding potentials (dashed contour lines) is switched off.

MD simulations are valuable tools if one wants to gain detailed insight into fast dynamical processes of proteins and other biological macromolecules at atomic resolution. But since conventional MD simulations are confined to the study of very fast processes, conformational flooding represents a complementary and powerful tool to predict and understand also slow conformational motions. Another obvious application is an enhanced refinement of Xray- or NMR-structures. 

Similar in spirit is the method of conformational flooding, which is used to study and to predict large-scale conformational motions in maaomolecular systems on a microsecond timescale. In this approach, the bias (flooding) potential can be applied to one intramolecular energy term only (e.g., torsional terms) so as not to destroy solvent stmcture around the maciomolecule. The bias potential dynamics, the bond-boost method, and the state-bridging bond-boost method are also variants of Voter s hyperdynamics. 

H. Grubmiiller, Phys. Rev. E, 52(3), 2893 (1995). Predicting Slow Structural Transitions in Macromolecular Systems Conformational Flooding. 

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