NOVEL ALGORITHMS FOR SEARCHING CONFORMATIONAL SPACE

The modelling of biological molecules by molecular dynamics is beset b y a range of problems. The most important of these is the multiple-min ima problem. The deep metastable minima can cause difficulties in prop er equilibration of a molecular system and result in the simulated sys tem being trapped in a long-lived metastable state. One way to overcom e these problems is to re-engineer the ''Newtonian Rules' in order to more efficiently search conformational space. Re-engineering of the 'N ewtonian Rules' implies a redesign of the physical laws arising from t hem. This is done in various ways by the RUSH, Hybrid Monte Carlo and PEACS algorithms. This paper explores applications of these algorithms , and compares them to a traditional molecular dynamics method.