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Disconnectivity graphs potential energy surfaces

Figure 1.3. Schematic examples of potential energy surfaces (potential energy as a function of some generalized coordinate) and the corresponding disconnectivity graphs. In each case, the dotted lines indicate the energy levels at which the superbasin analysis has been made, (a) A gently sloping funnel with high barriers ( willow tree ) (b) a steeper funnel with lower barriers ( palm tree ) and (c) a rough landscape ( banyan tree ). Figure 1.3. Schematic examples of potential energy surfaces (potential energy as a function of some generalized coordinate) and the corresponding disconnectivity graphs. In each case, the dotted lines indicate the energy levels at which the superbasin analysis has been made, (a) A gently sloping funnel with high barriers ( willow tree ) (b) a steeper funnel with lower barriers ( palm tree ) and (c) a rough landscape ( banyan tree ).
The next stage of realism beyond a lattice model is a continuum bead model, where atoms are grouped together into beads, and the beads are allowed to move continuously in space. Typically, one bead represents a single amino acid in a protein. All-atom representations of biomolecules constitute a further level of sophistication. In this final section of our review we investigate the potential energy surfaces of a continuum bead heteropolymer and a tetrapeptide modeled by an all atom potential. Disconnectivity graphs immediately provide a visual distinction between frustrated and unfrustrated systems in both cases. [Pg.90]

In this section we present disconnectivity graphs for an off-lattice model protein. The original model exhibits frustration [330] and does not fold efficiently to the global potential energy minimum. However, when the frustration is removed by constructing the corresponding G5-like model, the resulting surface resembles a funnel [158]. [Pg.90]


See other pages where Disconnectivity graphs potential energy surfaces is mentioned: [Pg.23]    [Pg.335]    [Pg.395]    [Pg.378]    [Pg.47]    [Pg.333]   
See also in sourсe #XX -- [ Pg.39 , Pg.40 , Pg.41 , Pg.42 , Pg.43 ]




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