Replica-exchange method using the generalized effective potential.
We propose an effective scheme for fast conformational searches by combining the replica exchange method (REM) with the generalized effect potential concept. The present method introduces the "q" value from the effective potential as a coupling parameter. It is found that the new method not only requires a much smaller number of replicas than the conventional REM, but also makes it possible to perform effective conformational sampling of complex systems with correct distributions maintained. The advantage of the present method has been demonstrated with in vacuo alanine dipeptide using a molecular dynamics simulation.
Jang
Soonmin
S
School of Chemistry, Seoul National University, Seoul 151-742, Korea.
Shin
Seokmin
S
Pak
Youngshang
Y
D003198:Computer Simulation; D004151:Dipeptides / Q000737:chemistry*; D008956:Models, Chemical; D011487:Protein Conformation; D013816:Thermodynamics; D014618:Vacuum
D004151:Dipeptides; C002956:alanylalanine