AMBER Archive (2009)
Subject: [AMBER] Verlet update time in explicit water Replica Exchange MD
From: Da-Wei Li (lidawei_at_gmail.com)
Date: Wed Nov 25 2009 - 11:05:55 CST
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?
AMBER mailing list