Biomolecules, potential energy surfaces

United atom force fields (see United versus All Atom Force Fields on page 28) are sometimes used for biomolecules to decrease the number of nonbonded interactions and the computation time. Another reason for using a simplified potential is to reduce the dimensionality of the potential energy surface. This, in turn, allows for more samples of the surface. 

Krivov, S.V. Chekmarev, S.F. Karplus, M., Potential energy surfaces and conformational transitions in biomolecules A successive confinement approach applied to a solvated tetrapeptide, Phys. Rev. Lett. 2002, 88, 038101... 

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. 

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