From: Jacob Usadi (jusadi_at_uchicago.edu)
Date: Fri Oct 20 2017 - 15:33:34 CDT
I wish to explore the conformational space of an oligomer formed by small
peptides (< 5 peptides of length <50 residues). The hope is that we will be
able to do this with full explicit detail, without resorting to implicit
solvent or coarse-graining.
The major limiting factor is that little detail is available on the
structure of the oligomer. Thus, metadynamics and methods that require
information about the structure at the outset are difficult. On the other
hand, those methods that allow conformational search without this sort of
initial information (like REMD, REST, etc) tend to be quite computationally
demanding, and may be a poor choice for oligomers in particular.
1) Are there conformational search methods that are particularly useful for
2) Are there methods that achieve balance between the high-information and
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