AMBER Archive (2009)

Subject: [AMBER] Verlet update time in explicit water Replica Exchange MD

From: Da-Wei Li (
Date: Wed Nov 25 2009 - 11:05:55 CST

Dear All:

I recently try explicit water replica exchange MD using Amber9. The md
run is very slow, compared with normal constant T runs. A close look
at the profile_mpi reveals that "Verlet update time" take about 3/4 of
the CPU times at processor 0. This is not normal. This does not happen
with constant T MD. I use CentOS and mvapich2.

Anyone has some idea?



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