Dimensional oscillation. A fast variation of energy embedding gives good results with the AMBER potential energy function.
The structure of the AMBER potential energy surface of the cyclic tetrapeptide cyclotetrasarcosyl is analyzed as a function of the dimensionality of coordinate space. It is found that the number of local energy minima decreases as the dimensionality of the space increases until some limit at which point equipotential subspaces appear. The applicability of energy embedding methods to finding global energy minima in this type of energy-conformation space is explored. Dimensional oscillation, a computationally fast variant of energy embedding is introduced and found to sample conformation space widely and to do a good job of finding global and near-global energy minima.
Snow
M E
ME
Scientific Computation Group, University of Michigan, Ann Arbor.
Crippen
G M
GM
D003198:Computer Simulation; D008432:Mathematical Computing; D008956:Models, Chemical; D008958:Models, Molecular; D010455:Peptides / Q000737:chemistry*; D010456:Peptides, Cyclic / Q000737:chemistry*; D011506:Proteins / Q000737:chemistry*; D012521:Sarcosine / Q000031:analogs & derivatives* / Q000737:chemistry
D010455:Peptides; D010456:Peptides, Cyclic; D011506:Proteins; C072880:cyclo(tetra(sarcosyl)); D012521:Sarcosine