Dear Amber Users,
During the course of an accelerated MD (aMD) of a small peptide I observed the formation/dissolution of an alpha-helix at a particular frequency. Is it possible to deduce from such aMD data that the frequency of (reversible) conformational change would be similar if the simulation was run without any acceleration? Or does aMD change the kinetics so substantially that the relative proportions of time spent in the folded and unfolded state would be quite different in "real time"?
The aMD simulations were run as specified in the Amber manual with the recommended alpha factor of 0.2.
ROJW
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Received on Fri Feb 05 2016 - 10:00:04 PST
