AMBER Archive (2008)

Subject: AMBER: NVE energy and temperature drift

From: Lars Skjærven (lars.skjarven_at_biomed.uib.no)
Date: Fri Mar 07 2008 - 09:36:48 CST

Dear Amber users,

This is a follow up question to a thread in 2007 regarding NVE simulations (
http://structbio.vanderbilt.edu/archives/amber-archive/2007/3178.php). I had
the same problem with energy drifting. Thus, I followed the recommendations
from Case and Cheatham; lower shake tolerance, increase the accuracy of the
PME by reducing DSUM_TOL by an order of magnitude, and dt=0.001. The
simulation is much "smoother" now in terms of energy and temperature. The
shift has now been reduced to 5 kcal/mol (-75489 to -75484, first to last
step) during a 10ns simulation. The energy does not yet seem to converge.

Should I be concerned about this energy drift, or is it small enough such
that I can accept it? My apologies if this has been answered earlier.

Best regards,
Lars Skjærven
Department of Biomedicine
University of Bergen
Norway

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