  The replica exchange molecular dynamics (REMD) approach is applied to four
oligomeric peptide systems. At physiologically relevant temperature values REMD
samples conformation space and aggregation transitions more efficiently than
constant temperature molecular dynamics (CTMD). During the aggregation process
the energetic and structural properties are essentially the same in REMD and
CTMD. A condensation stage toward disordered aggregates precedes the
$\beta$-sheet formation. Two order parameters, borrowed from anisotropic fluid
analysis, are used to monitor the aggregation process. The order parameters do
not depend on the peptide sequence and length and therefore allow to compare
the amyloidogenic propensity of different peptides.
