Paper Citing NAMD - Abstract
Grouleff, Julie; Jensen, Frank
Searching Peptide Conformational Space
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 7:1783-1790, JUN 2011
We have performed a near complete analysis of the conformational space in terms of minima and transition structures for four small peptide models with a force field energy function. There is a clear trend that minima having a large difference in structure, as measured by the distance in torsional space, are rarely connected by a single transition structure. There is a similar trend that activation energies for conformational transitions correlate with structure differences, such that small conformational changes occur with low energy barriers and vice versa. This suggests that a systematic search for low energy conformational transition structures should focus on pairs of minima that are structurally similar. Eigenvectors from diagonalization of force constant matrices at minima are better at describing conformational transitions than vibrational normal modes, as verified both by overlaps with geometry difference vectors and results from biased molecular dynamics simulations.
