AMBER Archive (2009)

Subject: [AMBER] Averaging simulations

From: Naser Alijabbari (
Date: Thu Apr 02 2009 - 10:21:41 CDT

When running multiple short MD simulation (using sander and AMBER10) using
different initial velocities (ntx=1, irest=0, ig=-1), does it make sense to
average the eigenvalues and eigenvectors from individual runs, as a means of
determining average properties? The idea would that by by somehow combining
individual trajectories one can also achieve Boltzmann sampling. But the
question is how does one combine individual trajectories.
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